Search results for the GEO ID: GSE29048  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM719994 | GPL1261 |
|
Intestine_KO_biological rep1
|
Mature proximal small intestine with intestinal epithelium-specific Pdx1 inactivation, first 5 cm immediately adjacent to the pylorus
|
gender: male
age: 6 months old
genotype: Pdx1flox/flox;VilCre (KO)
litter: brother of the same litter
|
Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.
|
| Sample_geo_accession | GSM719994
| | Sample_status | Public on Jan 12 2012
| | Sample_submission_date | May 04 2011
| | Sample_last_update_date | Jan 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice with intestinal epithelium-specific Pdx1 inactivation (Pdx1flox/flox;VilCre) were generated by intercross mating between VilCre and Pdx1flox/flox mouse strains. The VilCre mouse strain carries a Villin-Cre transgene and expresses Cre recombinase under the control of a 12.4 kb mouse villin 1 gene promoter fragment. Pdx1 exon 2 encoding the DNA-binding Homeodomain is flanked by loxP target sites in Pdx1flox/flox mice. Pdx1 expression is absent in the epithelium of mature Pdx1flox/flox;VilCre proximal small intestine.
| | Sample_growth_protocol_ch1 | Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The small intestine tissue was preserved in RNAlater (Qiagen, Valencia, CA) during harvest and before processing for RNA isolation. Total RNA was then extracted and treated with DNase I using the RNeasy Mini kit (Qiagen, Valencia, CA) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The total RNA samples were reverse transcribed into double-stranded cDNA, followed by an in vitro transcription (IVT) reaction that produced amplified amounts of biotin-labeled antisense mRNA (cRNA) using GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, CA), according to manufacturer’s recommendation.
| | Sample_hyb_protocol | The labeled cRNA prepared from each mouse was fragmented and hybridized to a single GeneChip Mouse Genome 430 2.0 Array (Affymetrix), according to manufacturer’s recommendation. The microarrays were washed, stained with fluorescent molecule SAPE that binds to biotin in combination of biotinylated anti-streptavidin antibody on GeneChip Fluidics Station 450 (Affymetrix).
| | Sample_scan_protocol | The arrays were scanned with GeneChip Scanner 3000 7G (Affymetrix).
| | Sample_data_processing | The fluorescence intensity image files obtained from scanning each of the arrays were reviewed and processed initially by the Stanford PAN Facility with GeneChip Operating Software (Affymetrix). The resulting .CEL files were imported into Partek Genomics Suite (version 6.4, Partek Inc., St. Louis, MO) for probe set summarization and statistical analysis.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Chin,,Chen
| | Sample_contact_email | chinchen@stanford.edu
| | Sample_contact_phone | 650-498-7599
| | Sample_contact_fax | 650-724-3106
| | Sample_contact_laboratory | Eric Sibley
| | Sample_contact_department | Pediatric Gastroenterology
| | Sample_contact_institute | Stanford University School of Medicine
| | Sample_contact_address | 300 Pasteur Drive
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305-5208
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM719nnn/GSM719994/suppl/GSM719994.CEL.gz
| | Sample_series_id | GSE29048
| | Sample_data_row_count | 45101
| | |
|
GSM719995 | GPL1261 |
|
Intestine_Ctrl_biological rep1
|
Mature proximal small intestine, first 5 cm immediately adjacent to the pylorus
|
gender: male
age: 6 months old
genotype: Pdx1flox/flox (Ctrl)
litter: brother of the same litter
|
Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.
|
| Sample_geo_accession | GSM719995
| | Sample_status | Public on Jan 12 2012
| | Sample_submission_date | May 04 2011
| | Sample_last_update_date | Jan 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice with intestinal epithelium-specific Pdx1 inactivation (Pdx1flox/flox;VilCre) were generated by intercross mating between VilCre and Pdx1flox/flox mouse strains. The VilCre mouse strain carries a Villin-Cre transgene and expresses Cre recombinase under the control of a 12.4 kb mouse villin 1 gene promoter fragment. Pdx1 exon 2 encoding the DNA-binding Homeodomain is flanked by loxP target sites in Pdx1flox/flox mice. Pdx1 expression is absent in the epithelium of mature Pdx1flox/flox;VilCre proximal small intestine.
| | Sample_growth_protocol_ch1 | Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The small intestine tissue was preserved in RNAlater (Qiagen, Valencia, CA) during harvest and before processing for RNA isolation. Total RNA was then extracted and treated with DNase I using the RNeasy Mini kit (Qiagen, Valencia, CA) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The total RNA samples were reverse transcribed into double-stranded cDNA, followed by an in vitro transcription (IVT) reaction that produced amplified amounts of biotin-labeled antisense mRNA (cRNA) using GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, CA), according to manufacturer’s recommendation.
| | Sample_hyb_protocol | The labeled cRNA prepared from each mouse was fragmented and hybridized to a single GeneChip Mouse Genome 430 2.0 Array (Affymetrix), according to manufacturer’s recommendation. The microarrays were washed, stained with fluorescent molecule SAPE that binds to biotin in combination of biotinylated anti-streptavidin antibody on GeneChip Fluidics Station 450 (Affymetrix).
| | Sample_scan_protocol | The arrays were scanned with GeneChip Scanner 3000 7G (Affymetrix).
| | Sample_data_processing | The fluorescence intensity image files obtained from scanning each of the arrays were reviewed and processed initially by the Stanford PAN Facility with GeneChip Operating Software (Affymetrix). The resulting .CEL files were imported into Partek Genomics Suite (version 6.4, Partek Inc., St. Louis, MO) for probe set summarization and statistical analysis.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Chin,,Chen
| | Sample_contact_email | chinchen@stanford.edu
| | Sample_contact_phone | 650-498-7599
| | Sample_contact_fax | 650-724-3106
| | Sample_contact_laboratory | Eric Sibley
| | Sample_contact_department | Pediatric Gastroenterology
| | Sample_contact_institute | Stanford University School of Medicine
| | Sample_contact_address | 300 Pasteur Drive
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305-5208
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM719nnn/GSM719995/suppl/GSM719995.CEL.gz
| | Sample_series_id | GSE29048
| | Sample_data_row_count | 45101
| | |
|
GSM719996 | GPL1261 |
|
Intestine_Ctrl_biological rep2
|
Mature proximal small intestine, first 5 cm immediately adjacent to the pylorus
|
gender: male
age: 6 months old
genotype: Pdx1flox/flox (Ctrl)
litter: brother of the same litter
|
Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.
|
| Sample_geo_accession | GSM719996
| | Sample_status | Public on Jan 12 2012
| | Sample_submission_date | May 04 2011
| | Sample_last_update_date | Jan 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice with intestinal epithelium-specific Pdx1 inactivation (Pdx1flox/flox;VilCre) were generated by intercross mating between VilCre and Pdx1flox/flox mouse strains. The VilCre mouse strain carries a Villin-Cre transgene and expresses Cre recombinase under the control of a 12.4 kb mouse villin 1 gene promoter fragment. Pdx1 exon 2 encoding the DNA-binding Homeodomain is flanked by loxP target sites in Pdx1flox/flox mice. Pdx1 expression is absent in the epithelium of mature Pdx1flox/flox;VilCre proximal small intestine.
| | Sample_growth_protocol_ch1 | Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The small intestine tissue was preserved in RNAlater (Qiagen, Valencia, CA) during harvest and before processing for RNA isolation. Total RNA was then extracted and treated with DNase I using the RNeasy Mini kit (Qiagen, Valencia, CA) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The total RNA samples were reverse transcribed into double-stranded cDNA, followed by an in vitro transcription (IVT) reaction that produced amplified amounts of biotin-labeled antisense mRNA (cRNA) using GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, CA), according to manufacturer’s recommendation.
| | Sample_hyb_protocol | The labeled cRNA prepared from each mouse was fragmented and hybridized to a single GeneChip Mouse Genome 430 2.0 Array (Affymetrix), according to manufacturer’s recommendation. The microarrays were washed, stained with fluorescent molecule SAPE that binds to biotin in combination of biotinylated anti-streptavidin antibody on GeneChip Fluidics Station 450 (Affymetrix).
| | Sample_scan_protocol | The arrays were scanned with GeneChip Scanner 3000 7G (Affymetrix).
| | Sample_data_processing | The fluorescence intensity image files obtained from scanning each of the arrays were reviewed and processed initially by the Stanford PAN Facility with GeneChip Operating Software (Affymetrix). The resulting .CEL files were imported into Partek Genomics Suite (version 6.4, Partek Inc., St. Louis, MO) for probe set summarization and statistical analysis.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Chin,,Chen
| | Sample_contact_email | chinchen@stanford.edu
| | Sample_contact_phone | 650-498-7599
| | Sample_contact_fax | 650-724-3106
| | Sample_contact_laboratory | Eric Sibley
| | Sample_contact_department | Pediatric Gastroenterology
| | Sample_contact_institute | Stanford University School of Medicine
| | Sample_contact_address | 300 Pasteur Drive
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305-5208
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM719nnn/GSM719996/suppl/GSM719996.CEL.gz
| | Sample_series_id | GSE29048
| | Sample_data_row_count | 45101
| | |
|
GSM719997 | GPL1261 |
|
Intestine_KO_biological rep2
|
Mature proximal small intestine with intestinal epithelium-specific Pdx1 inactivation, first 5 cm immediately adjacent to the pylorus
|
gender: male
age: 6 months old
genotype: Pdx1flox/flox;VilCre (KO)
litter: brother of the same litter
|
Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.
|
| Sample_geo_accession | GSM719997
| | Sample_status | Public on Jan 12 2012
| | Sample_submission_date | May 04 2011
| | Sample_last_update_date | Jan 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice with intestinal epithelium-specific Pdx1 inactivation (Pdx1flox/flox;VilCre) were generated by intercross mating between VilCre and Pdx1flox/flox mouse strains. The VilCre mouse strain carries a Villin-Cre transgene and expresses Cre recombinase under the control of a 12.4 kb mouse villin 1 gene promoter fragment. Pdx1 exon 2 encoding the DNA-binding Homeodomain is flanked by loxP target sites in Pdx1flox/flox mice. Pdx1 expression is absent in the epithelium of mature Pdx1flox/flox;VilCre proximal small intestine.
| | Sample_growth_protocol_ch1 | Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The small intestine tissue was preserved in RNAlater (Qiagen, Valencia, CA) during harvest and before processing for RNA isolation. Total RNA was then extracted and treated with DNase I using the RNeasy Mini kit (Qiagen, Valencia, CA) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The total RNA samples were reverse transcribed into double-stranded cDNA, followed by an in vitro transcription (IVT) reaction that produced amplified amounts of biotin-labeled antisense mRNA (cRNA) using GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, CA), according to manufacturer’s recommendation.
| | Sample_hyb_protocol | The labeled cRNA prepared from each mouse was fragmented and hybridized to a single GeneChip Mouse Genome 430 2.0 Array (Affymetrix), according to manufacturer’s recommendation. The microarrays were washed, stained with fluorescent molecule SAPE that binds to biotin in combination of biotinylated anti-streptavidin antibody on GeneChip Fluidics Station 450 (Affymetrix).
| | Sample_scan_protocol | The arrays were scanned with GeneChip Scanner 3000 7G (Affymetrix).
| | Sample_data_processing | The fluorescence intensity image files obtained from scanning each of the arrays were reviewed and processed initially by the Stanford PAN Facility with GeneChip Operating Software (Affymetrix). The resulting .CEL files were imported into Partek Genomics Suite (version 6.4, Partek Inc., St. Louis, MO) for probe set summarization and statistical analysis.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Chin,,Chen
| | Sample_contact_email | chinchen@stanford.edu
| | Sample_contact_phone | 650-498-7599
| | Sample_contact_fax | 650-724-3106
| | Sample_contact_laboratory | Eric Sibley
| | Sample_contact_department | Pediatric Gastroenterology
| | Sample_contact_institute | Stanford University School of Medicine
| | Sample_contact_address | 300 Pasteur Drive
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305-5208
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM719nnn/GSM719997/suppl/GSM719997.CEL.gz
| | Sample_series_id | GSE29048
| | Sample_data_row_count | 45101
| | |
|
GSM719998 | GPL1261 |
|
Intestine_KO_biological rep3
|
Mature proximal small intestine with intestinal epithelium-specific Pdx1 inactivation, first 5 cm immediately adjacent to the pylorus
|
gender: male
age: 6 months old
genotype: Pdx1flox/flox;VilCre (KO)
litter: brother of the same litter
|
Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.
|
| Sample_geo_accession | GSM719998
| | Sample_status | Public on Jan 12 2012
| | Sample_submission_date | May 04 2011
| | Sample_last_update_date | Jan 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice with intestinal epithelium-specific Pdx1 inactivation (Pdx1flox/flox;VilCre) were generated by intercross mating between VilCre and Pdx1flox/flox mouse strains. The VilCre mouse strain carries a Villin-Cre transgene and expresses Cre recombinase under the control of a 12.4 kb mouse villin 1 gene promoter fragment. Pdx1 exon 2 encoding the DNA-binding Homeodomain is flanked by loxP target sites in Pdx1flox/flox mice. Pdx1 expression is absent in the epithelium of mature Pdx1flox/flox;VilCre proximal small intestine.
| | Sample_growth_protocol_ch1 | Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The small intestine tissue was preserved in RNAlater (Qiagen, Valencia, CA) during harvest and before processing for RNA isolation. Total RNA was then extracted and treated with DNase I using the RNeasy Mini kit (Qiagen, Valencia, CA) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The total RNA samples were reverse transcribed into double-stranded cDNA, followed by an in vitro transcription (IVT) reaction that produced amplified amounts of biotin-labeled antisense mRNA (cRNA) using GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, CA), according to manufacturer’s recommendation.
| | Sample_hyb_protocol | The labeled cRNA prepared from each mouse was fragmented and hybridized to a single GeneChip Mouse Genome 430 2.0 Array (Affymetrix), according to manufacturer’s recommendation. The microarrays were washed, stained with fluorescent molecule SAPE that binds to biotin in combination of biotinylated anti-streptavidin antibody on GeneChip Fluidics Station 450 (Affymetrix).
| | Sample_scan_protocol | The arrays were scanned with GeneChip Scanner 3000 7G (Affymetrix).
| | Sample_data_processing | The fluorescence intensity image files obtained from scanning each of the arrays were reviewed and processed initially by the Stanford PAN Facility with GeneChip Operating Software (Affymetrix). The resulting .CEL files were imported into Partek Genomics Suite (version 6.4, Partek Inc., St. Louis, MO) for probe set summarization and statistical analysis.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Chin,,Chen
| | Sample_contact_email | chinchen@stanford.edu
| | Sample_contact_phone | 650-498-7599
| | Sample_contact_fax | 650-724-3106
| | Sample_contact_laboratory | Eric Sibley
| | Sample_contact_department | Pediatric Gastroenterology
| | Sample_contact_institute | Stanford University School of Medicine
| | Sample_contact_address | 300 Pasteur Drive
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305-5208
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM719nnn/GSM719998/suppl/GSM719998.CEL.gz
| | Sample_series_id | GSE29048
| | Sample_data_row_count | 45101
| | |
|
GSM719999 | GPL1261 |
|
Intestine_Ctrl_biological rep3
|
Mature proximal small intestine, first 5 cm immediately adjacent to the pylorus
|
gender: male
age: 6 months old
genotype: Pdx1flox/flox (Ctrl)
litter: brother of the same litter
|
Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.
|
| Sample_geo_accession | GSM719999
| | Sample_status | Public on Jan 12 2012
| | Sample_submission_date | May 04 2011
| | Sample_last_update_date | Jan 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice with intestinal epithelium-specific Pdx1 inactivation (Pdx1flox/flox;VilCre) were generated by intercross mating between VilCre and Pdx1flox/flox mouse strains. The VilCre mouse strain carries a Villin-Cre transgene and expresses Cre recombinase under the control of a 12.4 kb mouse villin 1 gene promoter fragment. Pdx1 exon 2 encoding the DNA-binding Homeodomain is flanked by loxP target sites in Pdx1flox/flox mice. Pdx1 expression is absent in the epithelium of mature Pdx1flox/flox;VilCre proximal small intestine.
| | Sample_growth_protocol_ch1 | Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The small intestine tissue was preserved in RNAlater (Qiagen, Valencia, CA) during harvest and before processing for RNA isolation. Total RNA was then extracted and treated with DNase I using the RNeasy Mini kit (Qiagen, Valencia, CA) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The total RNA samples were reverse transcribed into double-stranded cDNA, followed by an in vitro transcription (IVT) reaction that produced amplified amounts of biotin-labeled antisense mRNA (cRNA) using GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, CA), according to manufacturer’s recommendation.
| | Sample_hyb_protocol | The labeled cRNA prepared from each mouse was fragmented and hybridized to a single GeneChip Mouse Genome 430 2.0 Array (Affymetrix), according to manufacturer’s recommendation. The microarrays were washed, stained with fluorescent molecule SAPE that binds to biotin in combination of biotinylated anti-streptavidin antibody on GeneChip Fluidics Station 450 (Affymetrix).
| | Sample_scan_protocol | The arrays were scanned with GeneChip Scanner 3000 7G (Affymetrix).
| | Sample_data_processing | The fluorescence intensity image files obtained from scanning each of the arrays were reviewed and processed initially by the Stanford PAN Facility with GeneChip Operating Software (Affymetrix). The resulting .CEL files were imported into Partek Genomics Suite (version 6.4, Partek Inc., St. Louis, MO) for probe set summarization and statistical analysis.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Chin,,Chen
| | Sample_contact_email | chinchen@stanford.edu
| | Sample_contact_phone | 650-498-7599
| | Sample_contact_fax | 650-724-3106
| | Sample_contact_laboratory | Eric Sibley
| | Sample_contact_department | Pediatric Gastroenterology
| | Sample_contact_institute | Stanford University School of Medicine
| | Sample_contact_address | 300 Pasteur Drive
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305-5208
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM719nnn/GSM719999/suppl/GSM719999.CEL.gz
| | Sample_series_id | GSE29048
| | Sample_data_row_count | 45101
| | |
|
GSM720000 | GPL1261 |
|
Intestine_Ctrl_biological rep4
|
Mature proximal small intestine, first 5 cm immediately adjacent to the pylorus
|
gender: male
age: 6 months old
genotype: Pdx1flox/flox (Ctrl)
litter: brother of the same litter
|
Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.
|
| Sample_geo_accession | GSM720000
| | Sample_status | Public on Jan 12 2012
| | Sample_submission_date | May 04 2011
| | Sample_last_update_date | Jan 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice with intestinal epithelium-specific Pdx1 inactivation (Pdx1flox/flox;VilCre) were generated by intercross mating between VilCre and Pdx1flox/flox mouse strains. The VilCre mouse strain carries a Villin-Cre transgene and expresses Cre recombinase under the control of a 12.4 kb mouse villin 1 gene promoter fragment. Pdx1 exon 2 encoding the DNA-binding Homeodomain is flanked by loxP target sites in Pdx1flox/flox mice. Pdx1 expression is absent in the epithelium of mature Pdx1flox/flox;VilCre proximal small intestine.
| | Sample_growth_protocol_ch1 | Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The small intestine tissue was preserved in RNAlater (Qiagen, Valencia, CA) during harvest and before processing for RNA isolation. Total RNA was then extracted and treated with DNase I using the RNeasy Mini kit (Qiagen, Valencia, CA) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The total RNA samples were reverse transcribed into double-stranded cDNA, followed by an in vitro transcription (IVT) reaction that produced amplified amounts of biotin-labeled antisense mRNA (cRNA) using GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, CA), according to manufacturer’s recommendation.
| | Sample_hyb_protocol | The labeled cRNA prepared from each mouse was fragmented and hybridized to a single GeneChip Mouse Genome 430 2.0 Array (Affymetrix), according to manufacturer’s recommendation. The microarrays were washed, stained with fluorescent molecule SAPE that binds to biotin in combination of biotinylated anti-streptavidin antibody on GeneChip Fluidics Station 450 (Affymetrix).
| | Sample_scan_protocol | The arrays were scanned with GeneChip Scanner 3000 7G (Affymetrix).
| | Sample_data_processing | The fluorescence intensity image files obtained from scanning each of the arrays were reviewed and processed initially by the Stanford PAN Facility with GeneChip Operating Software (Affymetrix). The resulting .CEL files were imported into Partek Genomics Suite (version 6.4, Partek Inc., St. Louis, MO) for probe set summarization and statistical analysis.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Chin,,Chen
| | Sample_contact_email | chinchen@stanford.edu
| | Sample_contact_phone | 650-498-7599
| | Sample_contact_fax | 650-724-3106
| | Sample_contact_laboratory | Eric Sibley
| | Sample_contact_department | Pediatric Gastroenterology
| | Sample_contact_institute | Stanford University School of Medicine
| | Sample_contact_address | 300 Pasteur Drive
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305-5208
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM720nnn/GSM720000/suppl/GSM720000.CEL.gz
| | Sample_series_id | GSE29048
| | Sample_data_row_count | 45101
| | |
|
GSM720001 | GPL1261 |
|
Intestine_KO_biological rep4
|
Mature proximal small intestine with intestinal epithelium-specific Pdx1 inactivation, first 5 cm immediately adjacent to the pylorus
|
gender: male
age: 6 months old
genotype: Pdx1flox/flox;VilCre (KO)
litter: brother of the same litter
|
Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.
|
| Sample_geo_accession | GSM720001
| | Sample_status | Public on Jan 12 2012
| | Sample_submission_date | May 04 2011
| | Sample_last_update_date | Jan 12 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice with intestinal epithelium-specific Pdx1 inactivation (Pdx1flox/flox;VilCre) were generated by intercross mating between VilCre and Pdx1flox/flox mouse strains. The VilCre mouse strain carries a Villin-Cre transgene and expresses Cre recombinase under the control of a 12.4 kb mouse villin 1 gene promoter fragment. Pdx1 exon 2 encoding the DNA-binding Homeodomain is flanked by loxP target sites in Pdx1flox/flox mice. Pdx1 expression is absent in the epithelium of mature Pdx1flox/flox;VilCre proximal small intestine.
| | Sample_growth_protocol_ch1 | Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The small intestine tissue was preserved in RNAlater (Qiagen, Valencia, CA) during harvest and before processing for RNA isolation. Total RNA was then extracted and treated with DNase I using the RNeasy Mini kit (Qiagen, Valencia, CA) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The total RNA samples were reverse transcribed into double-stranded cDNA, followed by an in vitro transcription (IVT) reaction that produced amplified amounts of biotin-labeled antisense mRNA (cRNA) using GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, CA), according to manufacturer’s recommendation.
| | Sample_hyb_protocol | The labeled cRNA prepared from each mouse was fragmented and hybridized to a single GeneChip Mouse Genome 430 2.0 Array (Affymetrix), according to manufacturer’s recommendation. The microarrays were washed, stained with fluorescent molecule SAPE that binds to biotin in combination of biotinylated anti-streptavidin antibody on GeneChip Fluidics Station 450 (Affymetrix).
| | Sample_scan_protocol | The arrays were scanned with GeneChip Scanner 3000 7G (Affymetrix).
| | Sample_data_processing | The fluorescence intensity image files obtained from scanning each of the arrays were reviewed and processed initially by the Stanford PAN Facility with GeneChip Operating Software (Affymetrix). The resulting .CEL files were imported into Partek Genomics Suite (version 6.4, Partek Inc., St. Louis, MO) for probe set summarization and statistical analysis.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Chin,,Chen
| | Sample_contact_email | chinchen@stanford.edu
| | Sample_contact_phone | 650-498-7599
| | Sample_contact_fax | 650-724-3106
| | Sample_contact_laboratory | Eric Sibley
| | Sample_contact_department | Pediatric Gastroenterology
| | Sample_contact_institute | Stanford University School of Medicine
| | Sample_contact_address | 300 Pasteur Drive
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305-5208
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM720nnn/GSM720001/suppl/GSM720001.CEL.gz
| | Sample_series_id | GSE29048
| | Sample_data_row_count | 45101
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
