Result

Search results for the GEO ID: GSE20235

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Title

Source name

Description

Characteristics

GSM507146

GPL1261

glomerulus_wildtype_biological replicate 1

glomerulus wildtype control

genotype/variation: wildtype control gender: female age: 6 weeks tissue: glomerular isolation using magnetic bead perfusion

glomerulus_wildtype_biological replicate 1

Sample_geo_accession	GSM507146
Sample_status	Public on Aug 03 2010
Sample_submission_date	Feb 09 2010
Sample_last_update_date	Aug 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Three Pod-Cre fVHL mice and three littermate controls were selected for glomerular isolation using the magnetic bead technique (Takemoto M., et al., A new method for large scale isolation of kidney glomeruli from mice. Am J Pathol 2002, 161(3):799-805). Isolated glomeruli were washed three times with Hanks balanced salt solution, pelleted, flash frozen on dry ice and stored at -80oC until RNA isolation.
Sample_growth_protocol_ch1	Phenotyping protocol Litters were generated by crossing mice carrying both a single copy of Pod-Cre transgene (Moeller MJ et al., Podocyte-specific expression of cre recombinase in transgenic mice. Genesis 2003, 35(1):39-42) and homozygous for a floxed-modified von Hippel-Lindau locus (Haase VH et al.,Vascular tumors in livers with targeted inactivation of the von Hippel-Lindau tumor suppressor. Proc Natl Acad Sci U S A 2001 98(4):1583-1588). Urine was sampled by passive collection and a 6 microliter sample was separated on SDS-PAGE gel and stained with Commassie blue. Urine was diluted, based on SDS-PAGE results, and quantified by Exocell mouse albumin elisa. Animals were selected for the study with the Pod-Cre+ fVHL genotype and albumin levels ≤ the average of wildtype littermates.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total glomerular RNA was isolated using Qiagen RNeasy spin columns according to the manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared using Affymetrix GeneChip IVT Labeling kit according to the manufacturer’s instructions.
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Single scans were performed using the Affymetrix GeneChip 3000 scanner
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS5.0) on Affymetrix Data Mining Tool using Affymetrix default analysis settings as normalization method. http://www.affymetrix.com/support/technical/manual/expression_manual.affx
Sample_platform_id	GPL1261
Sample_contact_name	Brooke,M ,Steenhard
Sample_contact_email	bsteenhard@kumc.edu
Sample_contact_phone	913-588-2716
Sample_contact_fax	913-588-2710
Sample_contact_laboratory	Dr Dale R Abrahamson
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	Univ of KS Medical Center
Sample_contact_address	3901 Rainbow Blvd
Sample_contact_city	Kansas City
Sample_contact_state	KS
Sample_contact_zip/postal_code	66160
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507146/suppl/GSM507146.CEL.gz
Sample_series_id	GSE20235
Sample_data_row_count	45101

GSM507147

GPL1261

glomerulus_wildtype_biological replicate 2

glomerulus wildtype control

genotype/variation: wildtype control gender: female age: 6 weeks tissue: glomerular isolation using magnetic bead perfusion

glomerulus_wildtype_biological replicate 2

Sample_geo_accession	GSM507147
Sample_status	Public on Aug 03 2010
Sample_submission_date	Feb 09 2010
Sample_last_update_date	Aug 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Three Pod-Cre fVHL mice and three littermate controls were selected for glomerular isolation using the magnetic bead technique (Takemoto M., et al., A new method for large scale isolation of kidney glomeruli from mice. Am J Pathol 2002, 161(3):799-805). Isolated glomeruli were washed three times with Hanks balanced salt solution, pelleted, flash frozen on dry ice and stored at -80oC until RNA isolation.
Sample_growth_protocol_ch1	Phenotyping protocol Litters were generated by crossing mice carrying both a single copy of Pod-Cre transgene (Moeller MJ et al., Podocyte-specific expression of cre recombinase in transgenic mice. Genesis 2003, 35(1):39-42) and homozygous for a floxed-modified von Hippel-Lindau locus (Haase VH et al.,Vascular tumors in livers with targeted inactivation of the von Hippel-Lindau tumor suppressor. Proc Natl Acad Sci U S A 2001 98(4):1583-1588). Urine was sampled by passive collection and a 6 microliter sample was separated on SDS-PAGE gel and stained with Commassie blue. Urine was diluted, based on SDS-PAGE results, and quantified by Exocell mouse albumin elisa. Animals were selected for the study with the Pod-Cre+ fVHL genotype and albumin levels ≤ the average of wildtype littermates.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total glomerular RNA was isolated using Qiagen RNeasy spin columns according to the manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared using Affymetrix GeneChip IVT Labeling kit according to the manufacturer’s instructions.
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Single scans were performed using the Affymetrix GeneChip 3000 scanner
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS5.0) on Affymetrix Data Mining Tool using Affymetrix default analysis settings as normalization method. http://www.affymetrix.com/support/technical/manual/expression_manual.affx
Sample_platform_id	GPL1261
Sample_contact_name	Brooke,M ,Steenhard
Sample_contact_email	bsteenhard@kumc.edu
Sample_contact_phone	913-588-2716
Sample_contact_fax	913-588-2710
Sample_contact_laboratory	Dr Dale R Abrahamson
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	Univ of KS Medical Center
Sample_contact_address	3901 Rainbow Blvd
Sample_contact_city	Kansas City
Sample_contact_state	KS
Sample_contact_zip/postal_code	66160
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507147/suppl/GSM507147.CEL.gz
Sample_series_id	GSE20235
Sample_data_row_count	45101

GSM507148

GPL1261

glomerulus_wildtype_biological replicate 3

glomerulus wildtype control

genotype/variation: wildtype control gender: female age: 6 weeks tissue: glomerular isolation using magnetic bead perfusion

glomerulus_wildtype_biological replicate 3

Sample_geo_accession	GSM507148
Sample_status	Public on Aug 03 2010
Sample_submission_date	Feb 09 2010
Sample_last_update_date	Aug 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Three Pod-Cre fVHL mice and three littermate controls were selected for glomerular isolation using the magnetic bead technique (Takemoto M., et al., A new method for large scale isolation of kidney glomeruli from mice. Am J Pathol 2002, 161(3):799-805). Isolated glomeruli were washed three times with Hanks balanced salt solution, pelleted, flash frozen on dry ice and stored at -80oC until RNA isolation.
Sample_growth_protocol_ch1	Phenotyping protocol Litters were generated by crossing mice carrying both a single copy of Pod-Cre transgene (Moeller MJ et al., Podocyte-specific expression of cre recombinase in transgenic mice. Genesis 2003, 35(1):39-42) and homozygous for a floxed-modified von Hippel-Lindau locus (Haase VH et al.,Vascular tumors in livers with targeted inactivation of the von Hippel-Lindau tumor suppressor. Proc Natl Acad Sci U S A 2001 98(4):1583-1588). Urine was sampled by passive collection and a 6 microliter sample was separated on SDS-PAGE gel and stained with Commassie blue. Urine was diluted, based on SDS-PAGE results, and quantified by Exocell mouse albumin elisa. Animals were selected for the study with the Pod-Cre+ fVHL genotype and albumin levels ≤ the average of wildtype littermates.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total glomerular RNA was isolated using Qiagen RNeasy spin columns according to the manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared using Affymetrix GeneChip IVT Labeling kit according to the manufacturer’s instructions.
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Single scans were performed using the Affymetrix GeneChip 3000 scanner
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS5.0) on Affymetrix Data Mining Tool using Affymetrix default analysis settings as normalization method. http://www.affymetrix.com/support/technical/manual/expression_manual.affx
Sample_platform_id	GPL1261
Sample_contact_name	Brooke,M ,Steenhard
Sample_contact_email	bsteenhard@kumc.edu
Sample_contact_phone	913-588-2716
Sample_contact_fax	913-588-2710
Sample_contact_laboratory	Dr Dale R Abrahamson
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	Univ of KS Medical Center
Sample_contact_address	3901 Rainbow Blvd
Sample_contact_city	Kansas City
Sample_contact_state	KS
Sample_contact_zip/postal_code	66160
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507148/suppl/GSM507148.CEL.gz
Sample_series_id	GSE20235
Sample_data_row_count	45101

GSM507149

GPL1261

glomerulus_transgenic_biological replicate 1

glomerulus transgenic podocin-Cre excision of von Hippel-Lindau

genotype/variation: transgenic podocin-Cre excision of von Hippel-Lindau gender: female age: 6 weeks tissue: glomerular isolation using magnetic bead perfusion

glomerulus_transgenic_biological replicate 1

Sample_geo_accession	GSM507149
Sample_status	Public on Aug 03 2010
Sample_submission_date	Feb 09 2010
Sample_last_update_date	Aug 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Three Pod-Cre fVHL mice and three littermate controls were selected for glomerular isolation using the magnetic bead technique (Takemoto M., et al., A new method for large scale isolation of kidney glomeruli from mice. Am J Pathol 2002, 161(3):799-805). Isolated glomeruli were washed three times with Hanks balanced salt solution, pelleted, flash frozen on dry ice and stored at -80oC until RNA isolation.
Sample_growth_protocol_ch1	Phenotyping protocol Litters were generated by crossing mice carrying both a single copy of Pod-Cre transgene (Moeller MJ et al., Podocyte-specific expression of cre recombinase in transgenic mice. Genesis 2003, 35(1):39-42) and homozygous for a floxed-modified von Hippel-Lindau locus (Haase VH et al.,Vascular tumors in livers with targeted inactivation of the von Hippel-Lindau tumor suppressor. Proc Natl Acad Sci U S A 2001 98(4):1583-1588). Urine was sampled by passive collection and a 6 microliter sample was separated on SDS-PAGE gel and stained with Commassie blue. Urine was diluted, based on SDS-PAGE results, and quantified by Exocell mouse albumin elisa. Animals were selected for the study with the Pod-Cre+ fVHL genotype and albumin levels ≤ the average of wildtype littermates.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total glomerular RNA was isolated using Qiagen RNeasy spin columns according to the manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared using Affymetrix GeneChip IVT Labeling kit according to the manufacturer’s instructions.
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Single scans were performed using the Affymetrix GeneChip 3000 scanner
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS5.0) on Affymetrix Data Mining Tool using Affymetrix default analysis settings as normalization method. http://www.affymetrix.com/support/technical/manual/expression_manual.affx
Sample_platform_id	GPL1261
Sample_contact_name	Brooke,M ,Steenhard
Sample_contact_email	bsteenhard@kumc.edu
Sample_contact_phone	913-588-2716
Sample_contact_fax	913-588-2710
Sample_contact_laboratory	Dr Dale R Abrahamson
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	Univ of KS Medical Center
Sample_contact_address	3901 Rainbow Blvd
Sample_contact_city	Kansas City
Sample_contact_state	KS
Sample_contact_zip/postal_code	66160
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507149/suppl/GSM507149.CEL.gz
Sample_series_id	GSE20235
Sample_data_row_count	45101

GSM507150

GPL1261

glomerulus_transgenic_biological replicate 2

glomerulus transgenic podocin-Cre excision of von Hippel-Lindau

genotype/variation: transgenic podocin-Cre excision of von Hippel-Lindau gender: female age: 6 weeks tissue: glomerular isolation using magnetic bead perfusion

glomerulus_transgenic_biological replicate 2

Sample_geo_accession	GSM507150
Sample_status	Public on Aug 03 2010
Sample_submission_date	Feb 09 2010
Sample_last_update_date	Aug 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Three Pod-Cre fVHL mice and three littermate controls were selected for glomerular isolation using the magnetic bead technique (Takemoto M., et al., A new method for large scale isolation of kidney glomeruli from mice. Am J Pathol 2002, 161(3):799-805). Isolated glomeruli were washed three times with Hanks balanced salt solution, pelleted, flash frozen on dry ice and stored at -80oC until RNA isolation.
Sample_growth_protocol_ch1	Phenotyping protocol Litters were generated by crossing mice carrying both a single copy of Pod-Cre transgene (Moeller MJ et al., Podocyte-specific expression of cre recombinase in transgenic mice. Genesis 2003, 35(1):39-42) and homozygous for a floxed-modified von Hippel-Lindau locus (Haase VH et al.,Vascular tumors in livers with targeted inactivation of the von Hippel-Lindau tumor suppressor. Proc Natl Acad Sci U S A 2001 98(4):1583-1588). Urine was sampled by passive collection and a 6 microliter sample was separated on SDS-PAGE gel and stained with Commassie blue. Urine was diluted, based on SDS-PAGE results, and quantified by Exocell mouse albumin elisa. Animals were selected for the study with the Pod-Cre+ fVHL genotype and albumin levels ≤ the average of wildtype littermates.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total glomerular RNA was isolated using Qiagen RNeasy spin columns according to the manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared using Affymetrix GeneChip IVT Labeling kit according to the manufacturer’s instructions.
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Single scans were performed using the Affymetrix GeneChip 3000 scanner
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS5.0) on Affymetrix Data Mining Tool using Affymetrix default analysis settings as normalization method. http://www.affymetrix.com/support/technical/manual/expression_manual.affx
Sample_platform_id	GPL1261
Sample_contact_name	Brooke,M ,Steenhard
Sample_contact_email	bsteenhard@kumc.edu
Sample_contact_phone	913-588-2716
Sample_contact_fax	913-588-2710
Sample_contact_laboratory	Dr Dale R Abrahamson
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	Univ of KS Medical Center
Sample_contact_address	3901 Rainbow Blvd
Sample_contact_city	Kansas City
Sample_contact_state	KS
Sample_contact_zip/postal_code	66160
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507150/suppl/GSM507150.CEL.gz
Sample_series_id	GSE20235
Sample_data_row_count	45101

GSM507151

GPL1261

glomerulus_transgenic_biological replicate 3

glomerulus transgenic podocin-Cre excision of von Hippel-Lindau

genotype/variation: transgenic podocin-Cre excision of von Hippel-Lindau gender: female age: 6 weeks tissue: glomerular isolation using magnetic bead perfusion

glomerulus_transgenic_biological replicate 3

Sample_geo_accession	GSM507151
Sample_status	Public on Aug 03 2010
Sample_submission_date	Feb 09 2010
Sample_last_update_date	Aug 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Three Pod-Cre fVHL mice and three littermate controls were selected for glomerular isolation using the magnetic bead technique (Takemoto M., et al., A new method for large scale isolation of kidney glomeruli from mice. Am J Pathol 2002, 161(3):799-805). Isolated glomeruli were washed three times with Hanks balanced salt solution, pelleted, flash frozen on dry ice and stored at -80oC until RNA isolation.
Sample_growth_protocol_ch1	Phenotyping protocol Litters were generated by crossing mice carrying both a single copy of Pod-Cre transgene (Moeller MJ et al., Podocyte-specific expression of cre recombinase in transgenic mice. Genesis 2003, 35(1):39-42) and homozygous for a floxed-modified von Hippel-Lindau locus (Haase VH et al.,Vascular tumors in livers with targeted inactivation of the von Hippel-Lindau tumor suppressor. Proc Natl Acad Sci U S A 2001 98(4):1583-1588). Urine was sampled by passive collection and a 6 microliter sample was separated on SDS-PAGE gel and stained with Commassie blue. Urine was diluted, based on SDS-PAGE results, and quantified by Exocell mouse albumin elisa. Animals were selected for the study with the Pod-Cre+ fVHL genotype and albumin levels ≤ the average of wildtype littermates.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total glomerular RNA was isolated using Qiagen RNeasy spin columns according to the manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared using Affymetrix GeneChip IVT Labeling kit according to the manufacturer’s instructions.
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	Single scans were performed using the Affymetrix GeneChip 3000 scanner
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS5.0) on Affymetrix Data Mining Tool using Affymetrix default analysis settings as normalization method. http://www.affymetrix.com/support/technical/manual/expression_manual.affx
Sample_platform_id	GPL1261
Sample_contact_name	Brooke,M ,Steenhard
Sample_contact_email	bsteenhard@kumc.edu
Sample_contact_phone	913-588-2716
Sample_contact_fax	913-588-2710
Sample_contact_laboratory	Dr Dale R Abrahamson
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	Univ of KS Medical Center
Sample_contact_address	3901 Rainbow Blvd
Sample_contact_city	Kansas City
Sample_contact_state	KS
Sample_contact_zip/postal_code	66160
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM507nnn/GSM507151/suppl/GSM507151.CEL.gz
Sample_series_id	GSE20235
Sample_data_row_count	45101

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