Search results for the GEO ID: GSE6698  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM154540 | GPL339 |
|
Normal untreated mouse kidney, amplified total RNA, biological rep1
|
Normal untreated mouse kidney
|
Genotype: C57/BLACK6, males
Age: 7 weeks, body weight appr. 20g
|
Gene expression data from normal mouse kidneys.
|
| Sample_geo_accession | GSM154540
| | Sample_status | Public on Jan 16 2007
| | Sample_submission_date | Jan 10 2007
| | Sample_last_update_date | Jan 10 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Untreated normal mice were injected ip with 200µM s4U (bi-distilled water as control) together with 34µCi 3H-cytidine (20Ci/mmol; ARC) in a total volume of 1ml of 0.9% NaCl solution. At time 0+1h, injection was repeated. At time 0+2h, mice were sacrificed and kidneys removed for histopathologic examination and RNA isolation.
| | Sample_growth_protocol_ch1 | Mice were grown under standard conditions with free access to nutrition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to the Qiagen RNeasy Midi protocol. RNA quality and yield were measured by the RNA6000 Nano assay (Bioanalyzer 2100, Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed, linearly amplified as described previously (Kenzelmann M. et al. (2004), Genomics 83, 550-558.), and biotin-labelled via a T7-based strategy according to manufacturer's instructions (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10µg of cRNA were hybridized to MOE430A GeneChip (Affymetrix) according to manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G System (Affymetrix).
| | Sample_data_processing | The data were analyzed with the SAS MicroArray Solution 1.0, using standard settings except the following: consistence within experimental groups (stimulus and labelling combination) was determined by array group correlation. Loglinear mixed models with Bonferroni corrections were fitted for values of perfect-matches, only with stimulus (IRI-treatment) and labelling (s4U) considered to be constant and the chip-ID as random.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Marc,,Kenzelmann
| | Sample_contact_email | m.kenzelmann@dkfz.de
| | Sample_contact_phone | +41 31 632 3251
| | Sample_contact_fax | +41 31 632 3550
| | Sample_contact_department | Molecular Genome Analysis
| | Sample_contact_institute | Institute of Medical Microbiology, University of Bern
| | Sample_contact_address | Friedbuhlstrasse 51
| | Sample_contact_city | Bern
| | Sample_contact_zip/postal_code | 3010
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154540/suppl/GSM154540.cel.gz
| | Sample_series_id | GSE6698
| | Sample_data_row_count | 22690
| | |
|
GSM154541 | GPL339 |
|
Normal untreated mouse kidney, amplified total RNA, biological rep2
|
Normal untreated mouse kidney
|
Genotype: C57/BLACK6, males
Age: 7 weeks, body weight appr. 20g
|
Gene expression data from normal mouse kidneys.
|
| Sample_geo_accession | GSM154541
| | Sample_status | Public on Jan 16 2007
| | Sample_submission_date | Jan 10 2007
| | Sample_last_update_date | Jan 10 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Untreated normal mice were injected ip with 200µM s4U (bi-distilled water as control) together with 34µCi 3H-cytidine (20Ci/mmol; ARC) in a total volume of 1ml of 0.9% NaCl solution. At time 0+1h, injection was repeated. At time 0+2h, mice were sacrificed and kidneys removed for histopathologic examination and RNA isolation.
| | Sample_growth_protocol_ch1 | Mice were grown under standard conditions with free access to nutrition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to the Qiagen RNeasy Midi protocol. RNA quality and yield were measured by the RNA6000 Nano assay (Bioanalyzer 2100, Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed, linearly amplified as described previously (Kenzelmann M. et al. (2004), Genomics 83, 550-558.), and biotin-labelled via a T7-based strategy according to manufacturer's instructions (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10µg of cRNA were hybridized to MOE430A GeneChip (Affymetrix) according to manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G System (Affymetrix).
| | Sample_data_processing | The data were analyzed with the SAS MicroArray Solution 1.0, using standard settings except the following: consistence within experimental groups (stimulus and labelling combination) was determined by array group correlation. Loglinear mixed models with Bonferroni corrections were fitted for values of perfect-matches, only with stimulus (IRI-treatment) and labelling (s4U) considered to be constant and the chip-ID as random.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Marc,,Kenzelmann
| | Sample_contact_email | m.kenzelmann@dkfz.de
| | Sample_contact_phone | +41 31 632 3251
| | Sample_contact_fax | +41 31 632 3550
| | Sample_contact_department | Molecular Genome Analysis
| | Sample_contact_institute | Institute of Medical Microbiology, University of Bern
| | Sample_contact_address | Friedbuhlstrasse 51
| | Sample_contact_city | Bern
| | Sample_contact_zip/postal_code | 3010
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154541/suppl/GSM154541.cel.gz
| | Sample_series_id | GSE6698
| | Sample_data_row_count | 22690
| | |
|
GSM154542 | GPL339 |
|
Contralateral (not clamped) untreated mouse kidney, amplified total RNA, biological rep1
|
Contralateral (not clamped) untreated mouse kidney
|
Genotype: C57/BLACK6, males
Age: 7 weeks, body weight appr. 20g
|
Gene expression data from contralateral (untreated) kidneys of Ischemia-Reperfusion-Injury mice (IRI-mice).
|
| Sample_geo_accession | GSM154542
| | Sample_status | Public on Jan 16 2007
| | Sample_submission_date | Jan 10 2007
| | Sample_last_update_date | Jan 10 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were anesthesized with diethylether. After flank incision, the renal artery and vein of the left kidney were occluded by a vascular clamp for 45 min. The clamp was removed, and the organ was allowed to reperfuse (time 0). Animals were allowed to recover with free access to nutrition. At time 0+1h, 200µM s4U (bi-distilled water as control) together with 34µCi 3H-cytidine (20Ci/mmol; ARC) were injected ip in a total volume of 1ml of 0.9% NaCl solution. At time 0+2h, injection was repeated. At time 0+3h, mice were sacrificed and contralateral (untreated) kidneys removed for histopathologic examination and RNA isolation.
| | Sample_growth_protocol_ch1 | Mice were grown under standard conditions with free access to nutrition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to the Qiagen RNeasy Midi protocol. RNA quality and yield were measured by the RNA6000 Nano assay (Bioanalyzer 2100, Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed, linearly amplified as described previously (Kenzelmann M. et al. (2004), Genomics 83, 550-558.), and biotin-labelled via a T7-based strategy according to manufacturer's instructions (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10µg of cRNA were hybridized to MOE430A GeneChip (Affymetrix) according to manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G System (Affymetrix).
| | Sample_data_processing | The data were analyzed with the SAS MicroArray Solution 1.0, using standard settings except the following: consistence within experimental groups (stimulus and labelling combination) was determined by array group correlation. Loglinear mixed models with Bonferroni corrections were fitted for values of perfect-matches, only with stimulus (IRI-treatment) and labelling (s4U) considered to be constant and the chip-ID as random.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Marc,,Kenzelmann
| | Sample_contact_email | m.kenzelmann@dkfz.de
| | Sample_contact_phone | +41 31 632 3251
| | Sample_contact_fax | +41 31 632 3550
| | Sample_contact_department | Molecular Genome Analysis
| | Sample_contact_institute | Institute of Medical Microbiology, University of Bern
| | Sample_contact_address | Friedbuhlstrasse 51
| | Sample_contact_city | Bern
| | Sample_contact_zip/postal_code | 3010
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154542/suppl/GSM154542.cel.gz
| | Sample_series_id | GSE6698
| | Sample_data_row_count | 22690
| | |
|
GSM154543 | GPL339 |
|
Contralateral (not clamped) untreated mouse kidney, amplified total RNA, biological rep2
|
Contralateral (not clamped) untreated mouse kidney
|
Genotype: C57/BLACK6, males
Age: 7 weeks, body weight appr. 20g
|
Gene expression data from contralateral (untreated) kidneys of Ischemia-Reperfusion-Injury mice (IRI-mice).
|
| Sample_geo_accession | GSM154543
| | Sample_status | Public on Jan 16 2007
| | Sample_submission_date | Jan 10 2007
| | Sample_last_update_date | Jan 10 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were anesthesized with diethylether. After flank incision, the renal artery and vein of the left kidney were occluded by a vascular clamp for 45 min. The clamp was removed, and the organ was allowed to reperfuse (time 0). Animals were allowed to recover with free access to nutrition. At time 0+1h, 200µM s4U (bi-distilled water as control) together with 34µCi 3H-cytidine (20Ci/mmol; ARC) were injected ip in a total volume of 1ml of 0.9% NaCl solution. At time 0+2h, injection was repeated. At time 0+3h, mice were sacrificed and contralateral (untreated) kidneys removed for histopathologic examination and RNA isolation.
| | Sample_growth_protocol_ch1 | Mice were grown under standard conditions with free access to nutrition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to the Qiagen RNeasy Midi protocol. RNA quality and yield were measured by the RNA6000 Nano assay (Bioanalyzer 2100, Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed, linearly amplified as described previously (Kenzelmann M. et al. (2004), Genomics 83, 550-558.), and biotin-labelled via a T7-based strategy according to manufacturer's instructions (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10µg of cRNA were hybridized to MOE430A GeneChip (Affymetrix) according to manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G System (Affymetrix).
| | Sample_data_processing | The data were analyzed with the SAS MicroArray Solution 1.0, using standard settings except the following: consistence within experimental groups (stimulus and labelling combination) was determined by array group correlation. Loglinear mixed models with Bonferroni corrections were fitted for values of perfect-matches, only with stimulus (IRI-treatment) and labelling (s4U) considered to be constant and the chip-ID as random.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Marc,,Kenzelmann
| | Sample_contact_email | m.kenzelmann@dkfz.de
| | Sample_contact_phone | +41 31 632 3251
| | Sample_contact_fax | +41 31 632 3550
| | Sample_contact_department | Molecular Genome Analysis
| | Sample_contact_institute | Institute of Medical Microbiology, University of Bern
| | Sample_contact_address | Friedbuhlstrasse 51
| | Sample_contact_city | Bern
| | Sample_contact_zip/postal_code | 3010
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154543/suppl/GSM154543.cel.gz
| | Sample_series_id | GSE6698
| | Sample_data_row_count | 22690
| | |
|
GSM154544 | GPL339 |
|
Normal untreated mouse kidney, newly transcribed RNA, biological rep1
|
Normal untreated mouse kidney
|
Genotype: C57/BLACK6, males
Age: 7 weeks, body weight appr. 20g
|
Gene expression data from normal mouse kidneys.
|
| Sample_geo_accession | GSM154544
| | Sample_status | Public on Jan 16 2007
| | Sample_submission_date | Jan 10 2007
| | Sample_last_update_date | Jan 10 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Untreated normal mice were injected ip with 200µM s4U (bi-distilled water as control) together with 34µCi 3H-cytidine (20Ci/mmol; ARC) in a total volume of 1ml of 0.9% NaCl solution. At time 0+1h, injection was repeated. At time 0+2h, mice were sacrificed and kidneys removed for histopathologic examination and RNA isolation.
| | Sample_growth_protocol_ch1 | Mice were grown under standard conditions with free access to nutrition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to the Qiagen RNeasy Midi protocol. RNA quality and yield were measured by the RNA6000 Nano assay (Bioanalyzer 2100, Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed, linearly amplified as described previously (Kenzelmann M. et al. (2004), Genomics 83, 550-558.), and biotin-labelled via a T7-based strategy according to manufacturer's instructions (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10µg of cRNA were hybridized to MOE430A GeneChip (Affymetrix) according to manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G System (Affymetrix).
| | Sample_data_processing | The data were analyzed with the SAS MicroArray Solution 1.0, using standard settings except the following: consistence within experimental groups (stimulus and labelling combination) was determined by array group correlation. Loglinear mixed models with Bonferroni corrections were fitted for values of perfect-matches, only with stimulus (IRI-treatment) and labelling (s4U) considered to be constant and the chip-ID as random.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Marc,,Kenzelmann
| | Sample_contact_email | m.kenzelmann@dkfz.de
| | Sample_contact_phone | +41 31 632 3251
| | Sample_contact_fax | +41 31 632 3550
| | Sample_contact_department | Molecular Genome Analysis
| | Sample_contact_institute | Institute of Medical Microbiology, University of Bern
| | Sample_contact_address | Friedbuhlstrasse 51
| | Sample_contact_city | Bern
| | Sample_contact_zip/postal_code | 3010
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154544/suppl/GSM154544.cel.gz
| | Sample_series_id | GSE6698
| | Sample_data_row_count | 22690
| | |
|
GSM154545 | GPL339 |
|
Contralateral (not clamped) untreated mouse kidney, newly transcribed RNA, biological rep1
|
Contralateral (not clamped) untreated mouse kidney
|
Genotype: C57/BLACK6, males
Age: 7 weeks, body weight appr. 20g
|
Gene expression data from contralateral (untreated) kidneys of Ischemia-Reperfusion-Injury mice (IRI-mice).
|
| Sample_geo_accession | GSM154545
| | Sample_status | Public on Jan 16 2007
| | Sample_submission_date | Jan 10 2007
| | Sample_last_update_date | Jan 10 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were anesthesized with diethylether. After flank incision, the renal artery and vein of the left kidney were occluded by a vascular clamp for 45 min. The clamp was removed, and the organ was allowed to reperfuse (time 0). Animals were allowed to recover with free access to nutrition. At time 0+1h, 200µM s4U (bi-distilled water as control) together with 34µCi 3H-cytidine (20Ci/mmol; ARC) were injected ip in a total volume of 1ml of 0.9% NaCl solution. At time 0+2h, injection was repeated. At time 0+3h, mice were sacrificed and contralateral (untreated) kidneys removed for histopathologic examination and RNA isolation.
| | Sample_growth_protocol_ch1 | Mice were grown under standard conditions with free access to nutrition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to the Qiagen RNeasy Midi protocol. RNA quality and yield were measured by the RNA6000 Nano assay (Bioanalyzer 2100, Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed, linearly amplified as described previously (Kenzelmann M. et al. (2004), Genomics 83, 550-558.), and biotin-labelled via a T7-based strategy according to manufacturer's instructions (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10µg of cRNA were hybridized to MOE430A GeneChip (Affymetrix) according to manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G System (Affymetrix).
| | Sample_data_processing | The data were analyzed with the SAS MicroArray Solution 1.0, using standard settings except the following: consistence within experimental groups (stimulus and labelling combination) was determined by array group correlation. Loglinear mixed models with Bonferroni corrections were fitted for values of perfect-matches, only with stimulus (IRI-treatment) and labelling (s4U) considered to be constant and the chip-ID as random.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Marc,,Kenzelmann
| | Sample_contact_email | m.kenzelmann@dkfz.de
| | Sample_contact_phone | +41 31 632 3251
| | Sample_contact_fax | +41 31 632 3550
| | Sample_contact_department | Molecular Genome Analysis
| | Sample_contact_institute | Institute of Medical Microbiology, University of Bern
| | Sample_contact_address | Friedbuhlstrasse 51
| | Sample_contact_city | Bern
| | Sample_contact_zip/postal_code | 3010
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154545/suppl/GSM154545.cel.gz
| | Sample_series_id | GSE6698
| | Sample_data_row_count | 22690
| | |
|
GSM154546 | GPL339 |
|
Normal untreated mouse kidney, total RNA, biological rep1
|
Normal untreated mouse kidney
|
Genotype: C57/BLACK6, males
Age: 7 weeks, body weight appr. 20g
|
Gene expression data from normal mouse kidneys.
|
| Sample_geo_accession | GSM154546
| | Sample_status | Public on Jan 16 2007
| | Sample_submission_date | Jan 10 2007
| | Sample_last_update_date | Jan 10 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Untreated normal mice were injected ip with 200µM s4U (bi-distilled water as control) together with 34µCi 3H-cytidine (20Ci/mmol; ARC) in a total volume of 1ml of 0.9% NaCl solution. At time 0+1h, injection was repeated. At time 0+2h, mice were sacrificed and kidneys removed for histopathologic examination and RNA isolation.
| | Sample_growth_protocol_ch1 | Mice were grown under standard conditions with free access to nutrition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to the Qiagen RNeasy Midi protocol. RNA quality and yield were measured by the RNA6000 Nano assay (Bioanalyzer 2100, Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed, linearly amplified as described previously (Kenzelmann M. et al. (2004), Genomics 83, 550-558.), and biotin-labelled via a T7-based strategy according to manufacturer's instructions (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10µg of cRNA were hybridized to MOE430A GeneChip (Affymetrix) according to manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G System (Affymetrix).
| | Sample_data_processing | The data were analyzed with the SAS MicroArray Solution 1.0, using standard settings except the following: consistence within experimental groups (stimulus and labelling combination) was determined by array group correlation. Loglinear mixed models with Bonferroni corrections were fitted for values of perfect-matches, only with stimulus (IRI-treatment) and labelling (s4U) considered to be constant and the chip-ID as random.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Marc,,Kenzelmann
| | Sample_contact_email | m.kenzelmann@dkfz.de
| | Sample_contact_phone | +41 31 632 3251
| | Sample_contact_fax | +41 31 632 3550
| | Sample_contact_department | Molecular Genome Analysis
| | Sample_contact_institute | Institute of Medical Microbiology, University of Bern
| | Sample_contact_address | Friedbuhlstrasse 51
| | Sample_contact_city | Bern
| | Sample_contact_zip/postal_code | 3010
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154546/suppl/GSM154546.cel.gz
| | Sample_series_id | GSE6698
| | Sample_data_row_count | 22690
| | |
|
GSM154547 | GPL339 |
|
Normal untreated mouse kidney, total RNA, biological rep2
|
Normal untreated mouse kidney
|
Genotype: C57/BLACK6, males
Age: 7 weeks, body weight appr. 20g
|
Gene expression data from normal mouse kidneys.
|
| Sample_geo_accession | GSM154547
| | Sample_status | Public on Jan 16 2007
| | Sample_submission_date | Jan 10 2007
| | Sample_last_update_date | Jan 10 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Untreated normal mice were injected ip with 200µM s4U (bi-distilled water as control) together with 34µCi 3H-cytidine (20Ci/mmol; ARC) in a total volume of 1ml of 0.9% NaCl solution. At time 0+1h, injection was repeated. At time 0+2h, mice were sacrificed and kidneys removed for histopathologic examination and RNA isolation.
| | Sample_growth_protocol_ch1 | Mice were grown under standard conditions with free access to nutrition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to the Qiagen RNeasy Midi protocol. RNA quality and yield were measured by the RNA6000 Nano assay (Bioanalyzer 2100, Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed, linearly amplified as described previously (Kenzelmann M. et al. (2004), Genomics 83, 550-558.), and biotin-labelled via a T7-based strategy according to manufacturer's instructions (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10µg of cRNA were hybridized to MOE430A GeneChip (Affymetrix) according to manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G System (Affymetrix).
| | Sample_data_processing | The data were analyzed with the SAS MicroArray Solution 1.0, using standard settings except the following: consistence within experimental groups (stimulus and labelling combination) was determined by array group correlation. Loglinear mixed models with Bonferroni corrections were fitted for values of perfect-matches, only with stimulus (IRI-treatment) and labelling (s4U) considered to be constant and the chip-ID as random.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Marc,,Kenzelmann
| | Sample_contact_email | m.kenzelmann@dkfz.de
| | Sample_contact_phone | +41 31 632 3251
| | Sample_contact_fax | +41 31 632 3550
| | Sample_contact_department | Molecular Genome Analysis
| | Sample_contact_institute | Institute of Medical Microbiology, University of Bern
| | Sample_contact_address | Friedbuhlstrasse 51
| | Sample_contact_city | Bern
| | Sample_contact_zip/postal_code | 3010
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154547/suppl/GSM154547.cel.gz
| | Sample_series_id | GSE6698
| | Sample_data_row_count | 22690
| | |
|
GSM154548 | GPL339 |
|
Contralateral (not clamped) untreated mouse kidney, total RNA, biological rep1
|
Contralateral (not clamped) untreated mouse kidney
|
Genotype: C57/BLACK6, males
Age: 7 weeks, body weight appr. 20g
|
Gene expression data from contralateral (untreated) kidneys of Ischemia-Reperfusion-Injury mice (IRI-mice).
|
| Sample_geo_accession | GSM154548
| | Sample_status | Public on Jan 16 2007
| | Sample_submission_date | Jan 10 2007
| | Sample_last_update_date | Jan 10 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were anesthesized with diethylether. After flank incision, the renal artery and vein of the left kidney were occluded by a vascular clamp for 45 min. The clamp was removed, and the organ was allowed to reperfuse (time 0). Animals were allowed to recover with free access to nutrition. At time 0+1h, 200µM s4U (bi-distilled water as control) together with 34µCi 3H-cytidine (20Ci/mmol; ARC) were injected ip in a total volume of 1ml of 0.9% NaCl solution. At time 0+2h, injection was repeated. At time 0+3h, mice were sacrificed and contralateral (untreated) kidneys removed for histopathologic examination and RNA isolation.
| | Sample_growth_protocol_ch1 | Mice were grown under standard conditions with free access to nutrition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to the Qiagen RNeasy Midi protocol. RNA quality and yield were measured by the RNA6000 Nano assay (Bioanalyzer 2100, Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed, linearly amplified as described previously (Kenzelmann M. et al. (2004), Genomics 83, 550-558.), and biotin-labelled via a T7-based strategy according to manufacturer's instructions (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10µg of cRNA were hybridized to MOE430A GeneChip (Affymetrix) according to manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G System (Affymetrix).
| | Sample_data_processing | The data were analyzed with the SAS MicroArray Solution 1.0, using standard settings except the following: consistence within experimental groups (stimulus and labelling combination) was determined by array group correlation. Loglinear mixed models with Bonferroni corrections were fitted for values of perfect-matches, only with stimulus (IRI-treatment) and labelling (s4U) considered to be constant and the chip-ID as random.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Marc,,Kenzelmann
| | Sample_contact_email | m.kenzelmann@dkfz.de
| | Sample_contact_phone | +41 31 632 3251
| | Sample_contact_fax | +41 31 632 3550
| | Sample_contact_department | Molecular Genome Analysis
| | Sample_contact_institute | Institute of Medical Microbiology, University of Bern
| | Sample_contact_address | Friedbuhlstrasse 51
| | Sample_contact_city | Bern
| | Sample_contact_zip/postal_code | 3010
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154548/suppl/GSM154548.cel.gz
| | Sample_series_id | GSE6698
| | Sample_data_row_count | 22690
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GSM154549 | GPL339 |
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Contralateral (not clamped) untreated mouse kidney, total RNA, biological rep2
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Contralateral (not clamped) untreated mouse kidney
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Genotype: C57/BLACK6, males
Age: 7 weeks, body weight appr. 20g
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Gene expression data from contralateral (untreated) kidneys of Ischemia-Reperfusion-Injury mice (IRI-mice).
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| Sample_geo_accession | GSM154549
| | Sample_status | Public on Jan 16 2007
| | Sample_submission_date | Jan 10 2007
| | Sample_last_update_date | Jan 10 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were anesthesized with diethylether. After flank incision, the renal artery and vein of the left kidney were occluded by a vascular clamp for 45 min. The clamp was removed, and the organ was allowed to reperfuse (time 0). Animals were allowed to recover with free access to nutrition. At time 0+1h, 200µM s4U (bi-distilled water as control) together with 34µCi 3H-cytidine (20Ci/mmol; ARC) were injected ip in a total volume of 1ml of 0.9% NaCl solution. At time 0+2h, injection was repeated. At time 0+3h, mice were sacrificed and contralateral (untreated) kidneys removed for histopathologic examination and RNA isolation.
| | Sample_growth_protocol_ch1 | Mice were grown under standard conditions with free access to nutrition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated according to the Qiagen RNeasy Midi protocol. RNA quality and yield were measured by the RNA6000 Nano assay (Bioanalyzer 2100, Agilent Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed, linearly amplified as described previously (Kenzelmann M. et al. (2004), Genomics 83, 550-558.), and biotin-labelled via a T7-based strategy according to manufacturer's instructions (Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10µg of cRNA were hybridized to MOE430A GeneChip (Affymetrix) according to manufacturer's instructions.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G System (Affymetrix).
| | Sample_data_processing | The data were analyzed with the SAS MicroArray Solution 1.0, using standard settings except the following: consistence within experimental groups (stimulus and labelling combination) was determined by array group correlation. Loglinear mixed models with Bonferroni corrections were fitted for values of perfect-matches, only with stimulus (IRI-treatment) and labelling (s4U) considered to be constant and the chip-ID as random.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Marc,,Kenzelmann
| | Sample_contact_email | m.kenzelmann@dkfz.de
| | Sample_contact_phone | +41 31 632 3251
| | Sample_contact_fax | +41 31 632 3550
| | Sample_contact_department | Molecular Genome Analysis
| | Sample_contact_institute | Institute of Medical Microbiology, University of Bern
| | Sample_contact_address | Friedbuhlstrasse 51
| | Sample_contact_city | Bern
| | Sample_contact_zip/postal_code | 3010
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM154nnn/GSM154549/suppl/GSM154549.cel.gz
| | Sample_series_id | GSE6698
| | Sample_data_row_count | 22690
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