Search results for the GEO ID: GSE10608  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM267291 | GPL1355 |
|
C(AA)_HT_biological rep1
|
Healthy renal tissue, vehicle control 1
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected healthy tubule
|
C(AA)_HT_biological rep1
|
| Sample_geo_accession | GSM267291
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267291/suppl/GSM267291.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267292 | GPL1355 |
|
C(AA)_HT_biological rep2
|
Healthy renal tissue, vehicle control 2
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected healthy tubule
|
C(AA)_HT_biological rep2
|
| Sample_geo_accession | GSM267292
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267292/suppl/GSM267292.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267293 | GPL1355 |
|
C(AA,OTA)_HT_biological rep3
|
Healthy renal tissue, vehicle control 3
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected healthy tubule
|
C(AA,OTA)_HT_biological rep3
|
| Sample_geo_accession | GSM267293
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267293/suppl/GSM267293.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267294 | GPL1355 |
|
C(AA)_bAT_biological rep1
|
Renal basophilic atypical tubule, vehicle control 1
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical tubules
|
C(AA)_bAT_biological rep1
|
| Sample_geo_accession | GSM267294
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267294/suppl/GSM267294.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267295 | GPL1355 |
|
C(AA)_bAT_biological rep2
|
Renal basophilic atypical tubule, vehicle control 2
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical tubules
|
C(AA)_bAT_biological rep2
|
| Sample_geo_accession | GSM267295
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267295/suppl/GSM267295.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267296 | GPL1355 |
|
C(AA)_bAT_biological rep3
|
Renal basophilic atypical tubule, vehicle control 3
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical tubules
|
C(AA)_bAT_biological rep3
|
| Sample_geo_accession | GSM267296
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267296/suppl/GSM267296.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267297 | GPL1355 |
|
C(AA)_bAH_biological rep1
|
Renal basophilic hyperplasia, vehicle control 1
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical hyperplasia
|
C(AA)_bAH_biological rep1
|
| Sample_geo_accession | GSM267297
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267297/suppl/GSM267297.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267298 | GPL1355 |
|
C(AA)_bAH_biological rep2
|
Renal basophilic hyperplasia, vehicle control 2
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical hyperplasia
|
C(AA)_bAH_biological rep2
|
| Sample_geo_accession | GSM267298
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267298/suppl/GSM267298.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267299 | GPL1355 |
|
C(AA)_bAH_biological rep3
|
Renal basophilic hyperplasia, vehicle control 3
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical hyperplasia
|
C(AA)_bAH_biological rep3
|
| Sample_geo_accession | GSM267299
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267299/suppl/GSM267299.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267300 | GPL1355 |
|
AA_HT_biological rep1
|
Healthy renal tissue, AA treated Eker rat 1
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected healthy tubule
|
AA_HT_biological rep1
|
| Sample_geo_accession | GSM267300
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267300/suppl/GSM267300.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267301 | GPL1355 |
|
AA_HT_biological rep2
|
Healthy renal tissue, AA treated Eker rat 2
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected healthy tubule
|
AA_HT_biological rep2
|
| Sample_geo_accession | GSM267301
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267301/suppl/GSM267301.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267302 | GPL1355 |
|
AA_HT_biological rep3
|
Healthy renal tissue, AA treated Eker rat 3
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected healthy tubule
|
AA_HT_biological rep3
|
| Sample_geo_accession | GSM267302
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267302/suppl/GSM267302.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267303 | GPL1355 |
|
AA_bAT_biological rep1
|
Renal basophilic atypical tubule, AA treated Eker rat 1
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical tubules
|
AA_bAT_biological rep1
|
| Sample_geo_accession | GSM267303
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267303/suppl/GSM267303.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267304 | GPL1355 |
|
AA_bAT_biological rep2
|
Renal basophilic atypical tubule, AA treated Eker rat 2
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical tubules
|
AA_bAT_biological rep2
|
| Sample_geo_accession | GSM267304
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267304/suppl/GSM267304.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267305 | GPL1355 |
|
AA_bAT_biological rep3
|
Renal basophilic atypical tubule, AA treated Eker rat 2
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical tubules
|
AA_bAT_biological rep3
|
| Sample_geo_accession | GSM267305
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267305/suppl/GSM267305.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267306 | GPL1355 |
|
AA_bAH_biological rep1
|
Renal basophilic hyperplasia, AA treated Eker rat 1
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical hyperplasia
|
AA_bAH_biological rep1
|
| Sample_geo_accession | GSM267306
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267306/suppl/GSM267306.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267307 | GPL1355 |
|
AA_bAH_biological rep2
|
Renal basophilic hyperplasia, AA treated Eker rat 2
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical hyperplasia
|
AA_bAH_biological rep2
|
| Sample_geo_accession | GSM267307
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267307/suppl/GSM267307.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267308 | GPL1355 |
|
AA_bAH_biological rep3
|
Renal basophilic hyperplasia, AA treated Eker rat 3
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical hyperplasia
|
AA_bAH_biological rep3
|
| Sample_geo_accession | GSM267308
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267308/suppl/GSM267308.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267309 | GPL1355 |
|
C(OTA)_HT_biological rep1
|
Healthy renal tissue, vehicle control 1
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected healthy tubule
|
C(OTA)_HT_biological rep1
|
| Sample_geo_accession | GSM267309
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267309/suppl/GSM267309.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267310 | GPL1355 |
|
C(OTA)_HT_biological rep2
|
Healthy renal tissue, vehicle control 2
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected healthy tubule
|
C(OTA)_HT_biological rep2
|
| Sample_geo_accession | GSM267310
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267310/suppl/GSM267310.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267312 | GPL1355 |
|
OTA_HT_biological rep1
|
Healthy renal tissue, OTA treated Eker rat 1
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected healthy tubule
|
OTA_HT_biological rep1
|
| Sample_geo_accession | GSM267312
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267312/suppl/GSM267312.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267313 | GPL1355 |
|
OTA_HT_biological rep2
|
Healthy renal tissue, OTA treated Eker rat 2
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected healthy tubule
|
OTA_HT_biological rep2
|
| Sample_geo_accession | GSM267313
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267313/suppl/GSM267313.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267314 | GPL1355 |
|
OTA_HT_biological rep3
|
Healthy renal tissue, OTA treated Eker rat 3
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected healthy tubule
|
OTA_HT_biological rep3
|
| Sample_geo_accession | GSM267314
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267314/suppl/GSM267314.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267315 | GPL1355 |
|
OTA_bAT_biological rep1
|
Renal basophilic atypical tubule, OTA treated Eker rat 1
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical tubules
|
OTA_bAT_biological rep1
|
| Sample_geo_accession | GSM267315
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267315/suppl/GSM267315.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267316 | GPL1355 |
|
OTA_bAT_biological rep2
|
Renal basophilic atypical tubule, OTA treated Eker rat 2
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical tubules
|
OTA_bAT_biological rep2
|
| Sample_geo_accession | GSM267316
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267316/suppl/GSM267316.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267317 | GPL1355 |
|
OTA_bAT_biological rep3
|
Renal basophilic atypical tubule, OTA treated Eker rat 2
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical tubules
|
OTA_bAT_biological rep3
|
| Sample_geo_accession | GSM267317
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267317/suppl/GSM267317.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267318 | GPL1355 |
|
OTA_bAH_biological rep1
|
Renal basophilic hyperplasia, OTA treated Eker rat 1
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical hyperplasia
|
OTA_bAH_biological rep1
|
| Sample_geo_accession | GSM267318
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267318/suppl/GSM267318.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267319 | GPL1355 |
|
OTA_bAH_biological rep2
|
Renal basophilic hyperplasia, OTA treated Eker rat 2
|
Strain: Tsc2 mutant Long Evans rats (Eker rats)
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical hyperplasia
|
OTA_bAH_biological rep2
|
| Sample_geo_accession | GSM267319
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267319/suppl/GSM267319.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
|
GSM267320 | GPL1355 |
|
OTA_bAH_biological rep3
|
Renal basophilic hyperplasia, OTA treated Eker rat 3
|
Strain: Tsc2 mutant Long Evans rats (Eker rats).
Gender: male.
Age: 6-8 weeks
Tissue: Kidney
Sample: microdissected renal basophilic atypical hyperplasia
|
OTA_bAH_biological rep3
|
| Sample_geo_accession | GSM267320
| | Sample_status | Public on Feb 20 2010
| | Sample_submission_date | Feb 22 2008
| | Sample_last_update_date | Jan 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Eker rats were gavaged with OTA (210µg/ kg BW) or AA (1mg/ kg BW), dissolved in 0.1M sodium bicarbonate at five days a week. Time-matched vehicle controls were gavaged with 0.1M sodium bicarbonate. After 6 months of treatment, isofluran-anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS animals. Kidneys were collected and snap frozen for cryosectioning and laser microdissection.
| | Sample_growth_protocol_ch1 | Male heterozygous Tsc2 mutant Eker rats were purchased at 6-8 weeks of age from the University of Texas MD Anderson Cancer Center, Smithville, USA. Groups of male rats were randomly assigned to dose groups and allowed to acclimatize to laboratory conditions for 4 weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the manufacturer's instructions: RNeasy Micro Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling kit protocol from 10ng total RNA according to manufacturer's instructions (Affymetrix, USA; GeneChip® Expression 3'-Amplification Reagents Two-Cycle cDNA Synthesis Kit).
| | Sample_hyb_protocol | According to the manufacturer’s instructions (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 3, 701027 rev1), fragmented cRNA samples were hybridized on Affymetrix Rat Genome RAE230A arrays.
| | Sample_scan_protocol | The stained Genechips were scanned with the GCS3000 Scanner according to the manufacturer’s instructions, using GCOS software Vers 1 (Affymetrix, USA; GeneChip® Expression Analysis, Section 2, Chapter 4, 701028 rev1)
| | Sample_data_processing | Dark and white spots, gradients and distortions were detected and corrected in the CEL file data using GeneData Expressionist Refiner software. Then the data were condensed using Mas 5 algorithms and scaled to a target intensity
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Daniel,R.,Dietrich
| | Sample_contact_email | daniel.dietrich@uni-konstanz.de
| | Sample_contact_phone | 0049-7531-883518
| | Sample_contact_fax | 0049-7531-883170
| | Sample_contact_department | Environmental Toxicology
| | Sample_contact_institute | University of Konstanz
| | Sample_contact_address | Jakob-Burckhardt-Str. 25
| | Sample_contact_city | Konstanz
| | Sample_contact_zip/postal_code | 78467
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM267nnn/GSM267320/suppl/GSM267320.CEL.gz
| | Sample_series_id | GSE10608
| | Sample_data_row_count | 31099
| | |
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Make groups for comparisons |
(2 groups will be compared at a time) |
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