Search results for the GEO ID: GSE21576  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM538808 | GPL1261 |
|
vil-Cre-Bcl9-/-/Bcl9l-/- tumor 258, mouse 04
|
laser dissected tumor tissue
|
strain: 129SvEv/C57BL/6/DBA/2 mixed background
genotype: vil-Cre-Bcl9-/-/Bcl9l-/-
sample id: KO_11_04_258
|
|
| Sample_geo_accession | GSM538808
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Apr 28 2010
| | Sample_last_update_date | May 04 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Segments of one cm length of colon were cut, washed in chilled PBS, embedded in OCT and frozen immediately. 14 µm frozen sections were mounted on Leica membranes (Leica Microsystems, Wetzlar, Germany) for laser dissection microscopy, fixed in ethanol and colored with Mayer’s hematoxylin. Membranes were rinsed in water and ethanol and air-dried. Samples were prepared using a laser-dissecting microscope (Leica Microsystems, MMI-Nikon).
| | Sample_growth_protocol_ch1 | 6-8- Week-old mice were exposed first to a single dose dimethylhydrazine (DMH, 44 mg/kg body weight), which is metabolized in the liver to carcinogenic azoxymethane (AOM), followed by 7 days oral administration of 2 % dextrane sulfate sodium (DSS) in the drinking water
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Microdissected samples from one mouse were pooled and total RNA extracted in 20µL using the PicoPure RNA Isolation Kit (MDS Analytical Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 30 ng of total RNA were amplified using the NuGEN WT-Ovation pico kit (NuGEN Inc., San Carlos, USA).
| | Sample_hyb_protocol | cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, USA).
| | Sample_scan_protocol | scanner GCS 3000, software was GCOS (GeneChip Operating Software 1.4)
| | Sample_data_processing | Robust multi-array averaging and quantile normalization were used to quantify gene expression (R, Bioconductor, RMA package).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Michel,,Aguet
| | Sample_contact_email | michel.aguet@epfl.ch
| | Sample_contact_phone | +41 21 314 7150
| | Sample_contact_laboratory | Aguet Lab
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | EPFL/ISREC
| | Sample_contact_address | Rue du Bugnon 25
| | Sample_contact_city | Lausanne
| | Sample_contact_zip/postal_code | 1011
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM538nnn/GSM538808/suppl/GSM538808.CEL.gz
| | Sample_series_id | GSE21576
| | Sample_series_id | GSE21603
| | Sample_data_row_count | 45101
| | |
|
GSM538809 | GPL1261 |
|
vil-Cre-Bcl9-/-/Bcl9l-/- tumor 257, mouse 02
|
laser dissected tumor tissue
|
strain: 129SvEv/C57BL/6/DBA/2 mixed background
genotype: vil-Cre-Bcl9-/-/Bcl9l-/-
sample id: KO_2_02_257
|
|
| Sample_geo_accession | GSM538809
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Apr 28 2010
| | Sample_last_update_date | May 04 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Segments of one cm length of colon were cut, washed in chilled PBS, embedded in OCT and frozen immediately. 14 µm frozen sections were mounted on Leica membranes (Leica Microsystems, Wetzlar, Germany) for laser dissection microscopy, fixed in ethanol and colored with Mayer’s hematoxylin. Membranes were rinsed in water and ethanol and air-dried. Samples were prepared using a laser-dissecting microscope (Leica Microsystems, MMI-Nikon).
| | Sample_growth_protocol_ch1 | 6-8- Week-old mice were exposed first to a single dose dimethylhydrazine (DMH, 44 mg/kg body weight), which is metabolized in the liver to carcinogenic azoxymethane (AOM), followed by 7 days oral administration of 2 % dextrane sulfate sodium (DSS) in the drinking water
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Microdissected samples from one mouse were pooled and total RNA extracted in 20µL using the PicoPure RNA Isolation Kit (MDS Analytical Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 30 ng of total RNA were amplified using the NuGEN WT-Ovation pico kit (NuGEN Inc., San Carlos, USA).
| | Sample_hyb_protocol | cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, USA).
| | Sample_scan_protocol | scanner GCS 3000, software was GCOS (GeneChip Operating Software 1.4)
| | Sample_data_processing | Robust multi-array averaging and quantile normalization were used to quantify gene expression (R, Bioconductor, RMA package).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Michel,,Aguet
| | Sample_contact_email | michel.aguet@epfl.ch
| | Sample_contact_phone | +41 21 314 7150
| | Sample_contact_laboratory | Aguet Lab
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | EPFL/ISREC
| | Sample_contact_address | Rue du Bugnon 25
| | Sample_contact_city | Lausanne
| | Sample_contact_zip/postal_code | 1011
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM538nnn/GSM538809/suppl/GSM538809.CEL.gz
| | Sample_series_id | GSE21576
| | Sample_series_id | GSE21603
| | Sample_data_row_count | 45101
| | |
|
GSM538810 | GPL1261 |
|
vil-Cre-Bcl9-/-/Bcl9l-/- tumor 256, mouse 02
|
laser dissected tumor tissue
|
strain: 129SvEv/C57BL/6/DBA/2 mixed background
genotype: vil-Cre-Bcl9-/-/Bcl9l-/-
sample id: KO_6_02_256
|
|
| Sample_geo_accession | GSM538810
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Apr 28 2010
| | Sample_last_update_date | May 04 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Segments of one cm length of colon were cut, washed in chilled PBS, embedded in OCT and frozen immediately. 14 µm frozen sections were mounted on Leica membranes (Leica Microsystems, Wetzlar, Germany) for laser dissection microscopy, fixed in ethanol and colored with Mayer’s hematoxylin. Membranes were rinsed in water and ethanol and air-dried. Samples were prepared using a laser-dissecting microscope (Leica Microsystems, MMI-Nikon).
| | Sample_growth_protocol_ch1 | 6-8- Week-old mice were exposed first to a single dose dimethylhydrazine (DMH, 44 mg/kg body weight), which is metabolized in the liver to carcinogenic azoxymethane (AOM), followed by 7 days oral administration of 2 % dextrane sulfate sodium (DSS) in the drinking water
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Microdissected samples from one mouse were pooled and total RNA extracted in 20µL using the PicoPure RNA Isolation Kit (MDS Analytical Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 30 ng of total RNA were amplified using the NuGEN WT-Ovation pico kit (NuGEN Inc., San Carlos, USA).
| | Sample_hyb_protocol | cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, USA).
| | Sample_scan_protocol | scanner GCS 3000, software was GCOS (GeneChip Operating Software 1.4)
| | Sample_data_processing | Robust multi-array averaging and quantile normalization were used to quantify gene expression (R, Bioconductor, RMA package).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Michel,,Aguet
| | Sample_contact_email | michel.aguet@epfl.ch
| | Sample_contact_phone | +41 21 314 7150
| | Sample_contact_laboratory | Aguet Lab
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | EPFL/ISREC
| | Sample_contact_address | Rue du Bugnon 25
| | Sample_contact_city | Lausanne
| | Sample_contact_zip/postal_code | 1011
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM538nnn/GSM538810/suppl/GSM538810.CEL.gz
| | Sample_series_id | GSE21576
| | Sample_series_id | GSE21603
| | Sample_data_row_count | 45101
| | |
|
GSM538811 | GPL1261 |
|
vil-Cre-Bcl9-/-/Bcl9l-/- tumor 195, mouse 99
|
laser dissected tumor tissue
|
strain: 129SvEv/C57BL/6/DBA/2 mixed background
genotype: vil-Cre-Bcl9-/-/Bcl9l-/-
sample id: KO_7_99_195
|
|
| Sample_geo_accession | GSM538811
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Apr 28 2010
| | Sample_last_update_date | May 04 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Segments of one cm length of colon were cut, washed in chilled PBS, embedded in OCT and frozen immediately. 14 µm frozen sections were mounted on Leica membranes (Leica Microsystems, Wetzlar, Germany) for laser dissection microscopy, fixed in ethanol and colored with Mayer’s hematoxylin. Membranes were rinsed in water and ethanol and air-dried. Samples were prepared using a laser-dissecting microscope (Leica Microsystems, MMI-Nikon).
| | Sample_growth_protocol_ch1 | 6-8- Week-old mice were exposed first to a single dose dimethylhydrazine (DMH, 44 mg/kg body weight), which is metabolized in the liver to carcinogenic azoxymethane (AOM), followed by 7 days oral administration of 2 % dextrane sulfate sodium (DSS) in the drinking water
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Microdissected samples from one mouse were pooled and total RNA extracted in 20µL using the PicoPure RNA Isolation Kit (MDS Analytical Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 30 ng of total RNA were amplified using the NuGEN WT-Ovation pico kit (NuGEN Inc., San Carlos, USA).
| | Sample_hyb_protocol | cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, USA).
| | Sample_scan_protocol | scanner GCS 3000, software was GCOS (GeneChip Operating Software 1.4)
| | Sample_data_processing | Robust multi-array averaging and quantile normalization were used to quantify gene expression (R, Bioconductor, RMA package).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Michel,,Aguet
| | Sample_contact_email | michel.aguet@epfl.ch
| | Sample_contact_phone | +41 21 314 7150
| | Sample_contact_laboratory | Aguet Lab
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | EPFL/ISREC
| | Sample_contact_address | Rue du Bugnon 25
| | Sample_contact_city | Lausanne
| | Sample_contact_zip/postal_code | 1011
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM538nnn/GSM538811/suppl/GSM538811.CEL.gz
| | Sample_series_id | GSE21576
| | Sample_series_id | GSE21603
| | Sample_data_row_count | 45101
| | |
|
GSM538812 | GPL1261 |
|
vil-Cre-Bcl9-/-/Bcl9l-/- tumor 255, mouse 04
|
laser dissected tumor tissue
|
strain: 129SvEv/C57BL/6/DBA/2 mixed background
genotype: vil-Cre-Bcl9-/-/Bcl9l-/-
sample id: KO_9_04_255
|
|
| Sample_geo_accession | GSM538812
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Apr 28 2010
| | Sample_last_update_date | May 04 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Segments of one cm length of colon were cut, washed in chilled PBS, embedded in OCT and frozen immediately. 14 µm frozen sections were mounted on Leica membranes (Leica Microsystems, Wetzlar, Germany) for laser dissection microscopy, fixed in ethanol and colored with Mayer’s hematoxylin. Membranes were rinsed in water and ethanol and air-dried. Samples were prepared using a laser-dissecting microscope (Leica Microsystems, MMI-Nikon).
| | Sample_growth_protocol_ch1 | 6-8- Week-old mice were exposed first to a single dose dimethylhydrazine (DMH, 44 mg/kg body weight), which is metabolized in the liver to carcinogenic azoxymethane (AOM), followed by 7 days oral administration of 2 % dextrane sulfate sodium (DSS) in the drinking water
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Microdissected samples from one mouse were pooled and total RNA extracted in 20µL using the PicoPure RNA Isolation Kit (MDS Analytical Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 30 ng of total RNA were amplified using the NuGEN WT-Ovation pico kit (NuGEN Inc., San Carlos, USA).
| | Sample_hyb_protocol | cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, USA).
| | Sample_scan_protocol | scanner GCS 3000, software was GCOS (GeneChip Operating Software 1.4)
| | Sample_data_processing | Robust multi-array averaging and quantile normalization were used to quantify gene expression (R, Bioconductor, RMA package).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Michel,,Aguet
| | Sample_contact_email | michel.aguet@epfl.ch
| | Sample_contact_phone | +41 21 314 7150
| | Sample_contact_laboratory | Aguet Lab
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | EPFL/ISREC
| | Sample_contact_address | Rue du Bugnon 25
| | Sample_contact_city | Lausanne
| | Sample_contact_zip/postal_code | 1011
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM538nnn/GSM538812/suppl/GSM538812.CEL.gz
| | Sample_series_id | GSE21576
| | Sample_series_id | GSE21603
| | Sample_data_row_count | 45101
| | |
|
GSM538813 | GPL1261 |
|
wildtype, tumor 254, mouse 72
|
laser dissected tumor tissue
|
strain: 129SvEv/C57BL/6/DBA/2 mixed background
genotype: wildtype
sample id: WT_1_72_254
|
|
| Sample_geo_accession | GSM538813
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Apr 28 2010
| | Sample_last_update_date | May 04 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Segments of one cm length of colon were cut, washed in chilled PBS, embedded in OCT and frozen immediately. 14 µm frozen sections were mounted on Leica membranes (Leica Microsystems, Wetzlar, Germany) for laser dissection microscopy, fixed in ethanol and colored with Mayer’s hematoxylin. Membranes were rinsed in water and ethanol and air-dried. Samples were prepared using a laser-dissecting microscope (Leica Microsystems, MMI-Nikon).
| | Sample_growth_protocol_ch1 | 6-8- Week-old mice were exposed first to a single dose dimethylhydrazine (DMH, 44 mg/kg body weight), which is metabolized in the liver to carcinogenic azoxymethane (AOM), followed by 7 days oral administration of 2 % dextrane sulfate sodium (DSS) in the drinking water
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Microdissected samples from one mouse were pooled and total RNA extracted in 20µL using the PicoPure RNA Isolation Kit (MDS Analytical Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 30 ng of total RNA were amplified using the NuGEN WT-Ovation pico kit (NuGEN Inc., San Carlos, USA).
| | Sample_hyb_protocol | cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, USA).
| | Sample_scan_protocol | scanner GCS 3000, software was GCOS (GeneChip Operating Software 1.4)
| | Sample_data_processing | Robust multi-array averaging and quantile normalization were used to quantify gene expression (R, Bioconductor, RMA package).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Michel,,Aguet
| | Sample_contact_email | michel.aguet@epfl.ch
| | Sample_contact_phone | +41 21 314 7150
| | Sample_contact_laboratory | Aguet Lab
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | EPFL/ISREC
| | Sample_contact_address | Rue du Bugnon 25
| | Sample_contact_city | Lausanne
| | Sample_contact_zip/postal_code | 1011
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM538nnn/GSM538813/suppl/GSM538813.CEL.gz
| | Sample_series_id | GSE21576
| | Sample_series_id | GSE21603
| | Sample_data_row_count | 45101
| | |
|
GSM538814 | GPL1261 |
|
wildtype, tumor 215, mouse 72
|
laser dissected tumor tissue
|
strain: 129SvEv/C57BL/6/DBA/2 mixed background
genotype: wildtype
sample id: WT_12_72_215
|
|
| Sample_geo_accession | GSM538814
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Apr 28 2010
| | Sample_last_update_date | May 04 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Segments of one cm length of colon were cut, washed in chilled PBS, embedded in OCT and frozen immediately. 14 µm frozen sections were mounted on Leica membranes (Leica Microsystems, Wetzlar, Germany) for laser dissection microscopy, fixed in ethanol and colored with Mayer’s hematoxylin. Membranes were rinsed in water and ethanol and air-dried. Samples were prepared using a laser-dissecting microscope (Leica Microsystems, MMI-Nikon).
| | Sample_growth_protocol_ch1 | 6-8- Week-old mice were exposed first to a single dose dimethylhydrazine (DMH, 44 mg/kg body weight), which is metabolized in the liver to carcinogenic azoxymethane (AOM), followed by 7 days oral administration of 2 % dextrane sulfate sodium (DSS) in the drinking water
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Microdissected samples from one mouse were pooled and total RNA extracted in 20µL using the PicoPure RNA Isolation Kit (MDS Analytical Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 30 ng of total RNA were amplified using the NuGEN WT-Ovation pico kit (NuGEN Inc., San Carlos, USA).
| | Sample_hyb_protocol | cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, USA).
| | Sample_scan_protocol | scanner GCS 3000, software was GCOS (GeneChip Operating Software 1.4)
| | Sample_data_processing | Robust multi-array averaging and quantile normalization were used to quantify gene expression (R, Bioconductor, RMA package).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Michel,,Aguet
| | Sample_contact_email | michel.aguet@epfl.ch
| | Sample_contact_phone | +41 21 314 7150
| | Sample_contact_laboratory | Aguet Lab
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | EPFL/ISREC
| | Sample_contact_address | Rue du Bugnon 25
| | Sample_contact_city | Lausanne
| | Sample_contact_zip/postal_code | 1011
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM538nnn/GSM538814/suppl/GSM538814.CEL.gz
| | Sample_series_id | GSE21576
| | Sample_series_id | GSE21603
| | Sample_data_row_count | 45101
| | |
|
GSM538815 | GPL1261 |
|
wildtype, tumor 216, mouse 72
|
laser dissected tumor tissue
|
strain: 129SvEv/C57BL/6/DBA/2 mixed background
genotype: wildtype
sample id: WT_13_72_216
|
|
| Sample_geo_accession | GSM538815
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Apr 28 2010
| | Sample_last_update_date | May 04 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Segments of one cm length of colon were cut, washed in chilled PBS, embedded in OCT and frozen immediately. 14 µm frozen sections were mounted on Leica membranes (Leica Microsystems, Wetzlar, Germany) for laser dissection microscopy, fixed in ethanol and colored with Mayer’s hematoxylin. Membranes were rinsed in water and ethanol and air-dried. Samples were prepared using a laser-dissecting microscope (Leica Microsystems, MMI-Nikon).
| | Sample_growth_protocol_ch1 | 6-8- Week-old mice were exposed first to a single dose dimethylhydrazine (DMH, 44 mg/kg body weight), which is metabolized in the liver to carcinogenic azoxymethane (AOM), followed by 7 days oral administration of 2 % dextrane sulfate sodium (DSS) in the drinking water
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Microdissected samples from one mouse were pooled and total RNA extracted in 20µL using the PicoPure RNA Isolation Kit (MDS Analytical Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 30 ng of total RNA were amplified using the NuGEN WT-Ovation pico kit (NuGEN Inc., San Carlos, USA).
| | Sample_hyb_protocol | cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, USA).
| | Sample_scan_protocol | scanner GCS 3000, software was GCOS (GeneChip Operating Software 1.4)
| | Sample_data_processing | Robust multi-array averaging and quantile normalization were used to quantify gene expression (R, Bioconductor, RMA package).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Michel,,Aguet
| | Sample_contact_email | michel.aguet@epfl.ch
| | Sample_contact_phone | +41 21 314 7150
| | Sample_contact_laboratory | Aguet Lab
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | EPFL/ISREC
| | Sample_contact_address | Rue du Bugnon 25
| | Sample_contact_city | Lausanne
| | Sample_contact_zip/postal_code | 1011
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM538nnn/GSM538815/suppl/GSM538815.CEL.gz
| | Sample_series_id | GSE21576
| | Sample_series_id | GSE21603
| | Sample_data_row_count | 45101
| | |
|
GSM538816 | GPL1261 |
|
wildtype, tumor 191, mouse 72
|
laser dissected tumor tissue
|
strain: 129SvEv/C57BL/6/DBA/2 mixed background
genotype: wildtype
sample id: WT_3_72_191
|
|
| Sample_geo_accession | GSM538816
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Apr 28 2010
| | Sample_last_update_date | May 04 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Segments of one cm length of colon were cut, washed in chilled PBS, embedded in OCT and frozen immediately. 14 µm frozen sections were mounted on Leica membranes (Leica Microsystems, Wetzlar, Germany) for laser dissection microscopy, fixed in ethanol and colored with Mayer’s hematoxylin. Membranes were rinsed in water and ethanol and air-dried. Samples were prepared using a laser-dissecting microscope (Leica Microsystems, MMI-Nikon).
| | Sample_growth_protocol_ch1 | 6-8- Week-old mice were exposed first to a single dose dimethylhydrazine (DMH, 44 mg/kg body weight), which is metabolized in the liver to carcinogenic azoxymethane (AOM), followed by 7 days oral administration of 2 % dextrane sulfate sodium (DSS) in the drinking water
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Microdissected samples from one mouse were pooled and total RNA extracted in 20µL using the PicoPure RNA Isolation Kit (MDS Analytical Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 30 ng of total RNA were amplified using the NuGEN WT-Ovation pico kit (NuGEN Inc., San Carlos, USA).
| | Sample_hyb_protocol | cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, USA).
| | Sample_scan_protocol | scanner GCS 3000, software was GCOS (GeneChip Operating Software 1.4)
| | Sample_data_processing | Robust multi-array averaging and quantile normalization were used to quantify gene expression (R, Bioconductor, RMA package).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Michel,,Aguet
| | Sample_contact_email | michel.aguet@epfl.ch
| | Sample_contact_phone | +41 21 314 7150
| | Sample_contact_laboratory | Aguet Lab
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | EPFL/ISREC
| | Sample_contact_address | Rue du Bugnon 25
| | Sample_contact_city | Lausanne
| | Sample_contact_zip/postal_code | 1011
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM538nnn/GSM538816/suppl/GSM538816.CEL.gz
| | Sample_series_id | GSE21576
| | Sample_series_id | GSE21603
| | Sample_data_row_count | 45101
| | |
|
GSM538817 | GPL1261 |
|
wildtype, tumor 229, mouse 82
|
laser dissected tumor tissue
|
strain: 129SvEv/C57BL/6/DBA/2 mixed background
genotype: wildtype
sample id: WT_8_82_229
|
|
| Sample_geo_accession | GSM538817
| | Sample_status | Public on Sep 01 2010
| | Sample_submission_date | Apr 28 2010
| | Sample_last_update_date | May 04 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Segments of one cm length of colon were cut, washed in chilled PBS, embedded in OCT and frozen immediately. 14 µm frozen sections were mounted on Leica membranes (Leica Microsystems, Wetzlar, Germany) for laser dissection microscopy, fixed in ethanol and colored with Mayer’s hematoxylin. Membranes were rinsed in water and ethanol and air-dried. Samples were prepared using a laser-dissecting microscope (Leica Microsystems, MMI-Nikon).
| | Sample_growth_protocol_ch1 | 6-8- Week-old mice were exposed first to a single dose dimethylhydrazine (DMH, 44 mg/kg body weight), which is metabolized in the liver to carcinogenic azoxymethane (AOM), followed by 7 days oral administration of 2 % dextrane sulfate sodium (DSS) in the drinking water
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Microdissected samples from one mouse were pooled and total RNA extracted in 20µL using the PicoPure RNA Isolation Kit (MDS Analytical Technologies).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 30 ng of total RNA were amplified using the NuGEN WT-Ovation pico kit (NuGEN Inc., San Carlos, USA).
| | Sample_hyb_protocol | cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, USA).
| | Sample_scan_protocol | scanner GCS 3000, software was GCOS (GeneChip Operating Software 1.4)
| | Sample_data_processing | Robust multi-array averaging and quantile normalization were used to quantify gene expression (R, Bioconductor, RMA package).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Michel,,Aguet
| | Sample_contact_email | michel.aguet@epfl.ch
| | Sample_contact_phone | +41 21 314 7150
| | Sample_contact_laboratory | Aguet Lab
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | EPFL/ISREC
| | Sample_contact_address | Rue du Bugnon 25
| | Sample_contact_city | Lausanne
| | Sample_contact_zip/postal_code | 1011
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM538nnn/GSM538817/suppl/GSM538817.CEL.gz
| | Sample_series_id | GSE21576
| | Sample_series_id | GSE21603
| | Sample_data_row_count | 45101
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