Search results for the GEO ID: GSE14328  |
(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 |
GSM357851 | GPL570 |
|
K_AR8
|
AR8 kidney allograft biopsy, acute rejection
|
kidney allograft biopsy, acute rejection
banff classification: Grade 1B
|
K_AR8
|
| Sample_geo_accession | GSM357851
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 06 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip one cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining step required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM357nnn/GSM357851/suppl/GSM357851.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM357859 | GPL570 |
|
K_AR9
|
AR9 kidney allograft biopsy, acute rejection
|
acute rejection
banff classification: Grade 1B
|
K_AR9
|
| Sample_geo_accession | GSM357859
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 06 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM357nnn/GSM357859/suppl/GSM357859.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM357860 | GPL570 |
|
K_AR6
|
AR6 kidney allograft biopsy, acute rejection
|
acute rejection
|
K_AR6
|
| Sample_geo_accession | GSM357860
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 06 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM357nnn/GSM357860/suppl/GSM357860.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM357861 | GPL570 |
|
K_AR16
|
AR16 kidney allograft biopsy, acute rejection
|
acute rejection
banff classification: Grade 1A
|
K_AR16
|
| Sample_geo_accession | GSM357861
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 06 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM357nnn/GSM357861/suppl/GSM357861.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM357862 | GPL570 |
|
K_AR13
|
AR13 kidney allograft biopsy, acute rejection
|
acute rejection
banff classification: Grade 1B
|
K_AR13
|
| Sample_geo_accession | GSM357862
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 06 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM357nnn/GSM357862/suppl/GSM357862.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM357863 | GPL570 |
|
K_STA3
|
STA3 kidney allograft biopsy, stable
|
stable
|
K_STA3
|
| Sample_geo_accession | GSM357863
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 06 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM357nnn/GSM357863/suppl/GSM357863.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358003 | GPL570 |
|
K_AR14
|
AR14 kidney allograft biopsy, acute rejection
|
acute rejection
banff classification: Grade 1A
|
K_AR14
|
| Sample_geo_accession | GSM358003
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358003/suppl/GSM358003.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358004 | GPL570 |
|
K_STA7
|
STA7 kidney allograft biopsy, stable
|
stable
|
K_STA7
|
| Sample_geo_accession | GSM358004
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358004/suppl/GSM358004.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358005 | GPL570 |
|
K_AR17
|
AR17 kidney allograft biopsy, acute rejection
|
acute rejection
banff classification: Grade 1A
|
K_AR17
|
| Sample_geo_accession | GSM358005
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358005/suppl/GSM358005.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358006 | GPL570 |
|
K_STA13
|
STA13 kidney allograft biopsy, stable
|
stable
|
K_STA13
|
| Sample_geo_accession | GSM358006
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358006/suppl/GSM358006.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358007 | GPL570 |
|
K_STA2
|
STA2 kidney allograft biopsy, stable
|
stable
|
K_STA2
|
| Sample_geo_accession | GSM358007
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358007/suppl/GSM358007.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358008 | GPL570 |
|
K_STA1
|
STA1 kidney allograft biopsy, stable
|
stable
|
K_STA1
|
| Sample_geo_accession | GSM358008
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358008/suppl/GSM358008.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358009 | GPL570 |
|
K_AR7
|
AR7 kidney allograft biopsy, acute rejection
|
acute rejection
|
K_AR7
|
| Sample_geo_accession | GSM358009
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358009/suppl/GSM358009.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358015 | GPL570 |
|
K_AR12
|
AR12 kidney allograft biopsy, acute rejection
|
acute rejection
banff classification: Grade 1B
|
K_AR12
|
| Sample_geo_accession | GSM358015
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358015/suppl/GSM358015.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358016 | GPL570 |
|
K_STA18
|
STA18 kidney allograft biopsy, stable
|
stable
|
K_STA18
|
| Sample_geo_accession | GSM358016
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358016/suppl/GSM358016.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358017 | GPL570 |
|
K_STA4
|
STA4 kidney allograft biopsy, stable
|
stable
|
K_STA4
|
| Sample_geo_accession | GSM358017
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358017/suppl/GSM358017.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358018 | GPL570 |
|
K_STA8
|
STA8 kidney allograft biopsy, stable
|
stable
|
K_STA8
|
| Sample_geo_accession | GSM358018
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358018/suppl/GSM358018.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358020 | GPL570 |
|
K_STA6
|
STA6 kidney allograft biopsy, stable
|
stable
|
K_STA6
|
| Sample_geo_accession | GSM358020
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358020/suppl/GSM358020.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358021 | GPL570 |
|
K_STA11
|
STA11 kidney allograft biopsy, stable
|
stable
|
K_STA11
|
| Sample_geo_accession | GSM358021
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358021/suppl/GSM358021.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358258 | GPL570 |
|
K_STA5
|
STA5 kidney allograft biopsy, stable
|
stable
|
K_STA5
|
| Sample_geo_accession | GSM358258
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358258/suppl/GSM358258.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358259 | GPL570 |
|
K_AR18
|
AR18 kidney allograft biopsy, acute rejection
|
acute rejection
|
K_AR18
|
| Sample_geo_accession | GSM358259
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358259/suppl/GSM358259.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358265 | GPL570 |
|
K_AR2
|
AR2 kidney allograft biopsy, acute rejection
|
acute rejection
banff classification: Grade 1B
|
K_AR2
|
| Sample_geo_accession | GSM358265
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358265/suppl/GSM358265.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358266 | GPL570 |
|
K_STA14
|
STA14 kidney allograft biopsy, stable
|
stable
|
K_STA14
|
| Sample_geo_accession | GSM358266
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358266/suppl/GSM358266.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358268 | GPL570 |
|
K_STA12
|
STA12 kidney allograft biopsy, stable
|
stable
|
K_STA12
|
| Sample_geo_accession | GSM358268
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358268/suppl/GSM358268.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358269 | GPL570 |
|
K_AR11
|
AR11 kidney allograft biopsy, acute rejection
|
acute rejection
banff classification: Grade 1A
|
K_AR11
|
| Sample_geo_accession | GSM358269
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358269/suppl/GSM358269.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358281 | GPL570 |
|
K_AR1
|
AR1 kidney allograft biopsy, acute rejection
|
acute rejection
banff classification: Grade 1B
|
K_AR1
|
| Sample_geo_accession | GSM358281
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358281/suppl/GSM358281.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358282 | GPL570 |
|
K_STA16
|
STA16 kidney allograft biopsy, stable
|
stable
|
K_STA16
|
| Sample_geo_accession | GSM358282
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358282/suppl/GSM358282.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358286 | GPL570 |
|
K_AR15
|
AR15 kidney allograft biopsy, acute rejection
|
acute rejection
banff classification: Grade 1A
|
K_AR15
|
| Sample_geo_accession | GSM358286
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358286/suppl/GSM358286.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358287 | GPL570 |
|
K_AR5
|
AR5 kidney allograft biopsy, acute rejection
|
acute rejection
banff classification: Grade 1B
|
K_AR5
|
| Sample_geo_accession | GSM358287
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358287/suppl/GSM358287.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358288 | GPL570 |
|
K_AR10
|
AR10 kidney allograft biopsy, acute rejection
|
acute rejection
banff classification: Grade 11A
|
K_AR10
|
| Sample_geo_accession | GSM358288
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358288/suppl/GSM358288.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358289 | GPL570 |
|
K_AR3
|
AR3 kidney allograft biopsy, acute rejection
|
acute rejection
banff classification: Grade 1B
|
K_AR3
|
| Sample_geo_accession | GSM358289
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358289/suppl/GSM358289.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358290 | GPL570 |
|
K_AR4
|
AR4 kidney allograft biopsy, acute rejection
|
acute rejection
banff classification: Grade 1B
|
K_AR4
|
| Sample_geo_accession | GSM358290
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358290/suppl/GSM358290.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358291 | GPL570 |
|
K_STA10
|
STA10 kidney allograft biopsy, stable
|
stable
|
K_STA10
|
| Sample_geo_accession | GSM358291
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358291/suppl/GSM358291.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358292 | GPL570 |
|
K_STA15
|
STA15 kidney allograft biopsy, stable
|
stable
|
K_STA15
|
| Sample_geo_accession | GSM358292
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358292/suppl/GSM358292.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358293 | GPL570 |
|
K_STA9
|
STA9_ kidney allograft biopsy, stable
|
stable
|
K_STA9
|
| Sample_geo_accession | GSM358293
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358293/suppl/GSM358293.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
GSM358294 | GPL570 |
|
K_STA17
|
STA17 kidney allograft biopsy, stable
|
stable
|
K_STA17
|
| Sample_geo_accession | GSM358294
| | Sample_status | Public on Oct 12 2010
| | Sample_submission_date | Jan 07 2009
| | Sample_last_update_date | Oct 12 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 | For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | GeneChip One-cycle target labeling and control reagents
| | Sample_hyb_protocol | 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays.
| | Sample_hyb_protocol | 2. Equilibrate probe array to room temperature immediately before use.
| | Sample_hyb_protocol | 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block.
| | Sample_hyb_protocol | 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa.
| | Sample_hyb_protocol | 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes.
| | Sample_hyb_protocol | 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture.
| | Sample_hyb_protocol | 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2).
| | Sample_hyb_protocol | 9. Place probe array into the hybridization oven, set to 45°C.
| | Sample_hyb_protocol | 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm.
| | Sample_hyb_protocol | 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.
| | Sample_scan_protocol | 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
| | Sample_scan_protocol | 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list.
| | Sample_scan_protocol | 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
| | Sample_scan_protocol | 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner.
| | Sample_scan_protocol | 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam.
| | Sample_scan_protocol = • Pixel value | 3 μm
| | Sample_scan_protocol = • Wavelength | 570 nm
| | Sample_scan_protocol | If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
| | Sample_scan_protocol | 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode.
| | Sample_scan_protocol | 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.
| | Sample_data_processing | Dchip MBEI processing, quantile-quantile normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | l3li@stanford.edu
| | Sample_contact_phone | 6507243765
| | Sample_contact_laboratory | Sarwal Lab
| | Sample_contact_department | Pediatric
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | 300 pastuer dr.,
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358294/suppl/GSM358294.CEL.gz
| | Sample_series_id | GSE14328
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
