Search results for the GEO ID: GSE9226 |
(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 |
GSM234639 | GPL341 |
|
SpragueDawley-liver-control-rep1
|
control rat liver
|
Strain:Sprague/Dawley, Age:10-12 weeks, Tissue: liver, Gender: Male
|
Gene expression data from control rat liver
|
Sample_geo_accession | GSM234639
| Sample_status | Public on Nov 24 2009
| Sample_submission_date | Oct 04 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | No treatments were given.
| Sample_growth_protocol_ch1 | Male Sprague Dawley (SD) rats between the ages of 10 and 12 weeks were obtained from the breeding colonies of the National Public Health Institute, Division of Environmental Health, Kuopio, Finland. Rats were kept in stainless steel wire-mesh cages with unlimited access to standard animal feed (R36, Ewos, Södertälje, Sweden) and tap water. Lights were on between 7:00 and 19:00. Ambient room temperature and humidity were maintained at 21.5 ± 1 ?C and 55 ± 10%, respectively.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Liver was harvested, sliced, snap-frozen and stored in liquid nitrogen until homogenization. Total RNA was extracted using RNeasy kits (Qiagen) according to the manufacturer’s instructions. DNase (Qiagen) was added to the RNeasy elution column as recommended by the manufacturer. RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyser.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The isolated RNA was then assayed on Affymetrix RAE230-2 arrays at The Centre for Applied Genomics at The Hospital for Sick Children (Toronto, Canada) following standard manufacturer's protocols. That is, a total of 1.5 µg of purified total RNA template was reverse-transcribed to generate double-stranded cDNA. Following second strand cDNA synthesis, biotin-labeled antisense cRNA was generated by in vitro transcription. Next, 15 µg of each generated cRNA preparation was fragmented and hybridized to an Affymetrix RAE230-2 oliogonucleotide array. Automated washing, staining and scanning was done according to the manufacturer's protocols.
| Sample_hyb_protocol | The isolated RNA was then assayed on Affymetrix RAE230-2 arrays at The Centre for Applied Genomics at The Hospital for Sick Children (Toronto, Canada) following standard manufacturer's protocols. That is, a total of 1.5 µg of purified total RNA template was reverse-transcribed to generate double-stranded cDNA. Following second strand cDNA synthesis, biotin-labeled antisense cRNA was generated by in vitro transcription. Next, 15 µg of each generated cRNA preparation was fragmented and hybridized to an Affymetrix RAE230-2 oliogonucleotide array. Automated washing, staining and scanning was done according to the manufacturer's protocols.
| Sample_scan_protocol | The isolated RNA was then assayed on Affymetrix RAE230-2 arrays at The Centre for Applied Genomics at The Hospital for Sick Children (Toronto, Canada) following standard manufacturer's protocols. That is, a total of 1.5 µg of purified total RNA template was reverse-transcribed to generate double-stranded cDNA. Following second strand cDNA synthesis, biotin-labeled antisense cRNA was generated by in vitro transcription. Next, 15 µg of each generated cRNA preparation was fragmented and hybridized to an Affymetrix RAE230-2 oliogonucleotide array. Automated washing, staining and scanning was done according to the manufacturer's protocols.
| Sample_data_processing | Affymetrix array data were loaded into the R statistical environment (v2.4.1) using the affy package (v1.12.2) of the BioConductor open-source library (Gentleman et al., 2004). The raw data were then pre-processed using the GC-RMA variant (Wu et al., 2004) of the common RMA algorithm (Irizarry et al., 2003a), as implemented in the gcrma package of BioConductor (v2.6.0).
| Sample_platform_id | GPL341
| Sample_contact_name | Paul,C,Boutros
| Sample_contact_email | Paul.Boutros@utoronto.ca
| Sample_contact_institute | Ontario Institute for Cancer Research
| Sample_contact_address | 101 College Street, Suite 800
| Sample_contact_city | Toronto
| Sample_contact_state | Ontario
| Sample_contact_zip/postal_code | M5G 0A3
| Sample_contact_country | Canada
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234639/suppl/GSM234639.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234639/suppl/GSM234639.CHP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234639/suppl/GSM234639.DAT.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234639/suppl/GSM234639.EXP.gz
| Sample_series_id | GSE9226
| Sample_data_row_count | 15923
| |
|
GSM234640 | GPL341 |
|
SpragueDawley-liver-control-rep2
|
control rat liver
|
Strain:Sprague/Dawley, Age:10-12 weeks, Tissue: liver, Gender: Male
|
Gene expression data from control rat liver
|
Sample_geo_accession | GSM234640
| Sample_status | Public on Nov 24 2009
| Sample_submission_date | Oct 04 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | No treatments were given.
| Sample_growth_protocol_ch1 | Male Sprague Dawley (SD) rats between the ages of 10 and 12 weeks were obtained from the breeding colonies of the National Public Health Institute, Division of Environmental Health, Kuopio, Finland. Rats were kept in stainless steel wire-mesh cages with unlimited access to standard animal feed (R36, Ewos, Södertälje, Sweden) and tap water. Lights were on between 7:00 and 19:00. Ambient room temperature and humidity were maintained at 21.5 ± 1 ?C and 55 ± 10%, respectively.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Liver was harvested, sliced, snap-frozen and stored in liquid nitrogen until homogenization. Total RNA was extracted using RNeasy kits (Qiagen) according to the manufacturer’s instructions. DNase (Qiagen) was added to the RNeasy elution column as recommended by the manufacturer. RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyser.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The isolated RNA was then assayed on Affymetrix RAE230-2 arrays at The Centre for Applied Genomics at The Hospital for Sick Children (Toronto, Canada) following standard manufacturer's protocols. That is, a total of 1.5 µg of purified total RNA template was reverse-transcribed to generate double-stranded cDNA. Following second strand cDNA synthesis, biotin-labeled antisense cRNA was generated by in vitro transcription. Next, 15 µg of each generated cRNA preparation was fragmented and hybridized to an Affymetrix RAE230-2 oliogonucleotide array. Automated washing, staining and scanning was done according to the manufacturer's protocols.
| Sample_hyb_protocol | The isolated RNA was then assayed on Affymetrix RAE230-2 arrays at The Centre for Applied Genomics at The Hospital for Sick Children (Toronto, Canada) following standard manufacturer's protocols. That is, a total of 1.5 µg of purified total RNA template was reverse-transcribed to generate double-stranded cDNA. Following second strand cDNA synthesis, biotin-labeled antisense cRNA was generated by in vitro transcription. Next, 15 µg of each generated cRNA preparation was fragmented and hybridized to an Affymetrix RAE230-2 oliogonucleotide array. Automated washing, staining and scanning was done according to the manufacturer's protocols.
| Sample_scan_protocol | The isolated RNA was then assayed on Affymetrix RAE230-2 arrays at The Centre for Applied Genomics at The Hospital for Sick Children (Toronto, Canada) following standard manufacturer's protocols. That is, a total of 1.5 µg of purified total RNA template was reverse-transcribed to generate double-stranded cDNA. Following second strand cDNA synthesis, biotin-labeled antisense cRNA was generated by in vitro transcription. Next, 15 µg of each generated cRNA preparation was fragmented and hybridized to an Affymetrix RAE230-2 oliogonucleotide array. Automated washing, staining and scanning was done according to the manufacturer's protocols.
| Sample_data_processing | Affymetrix array data were loaded into the R statistical environment (v2.4.1) using the affy package (v1.12.2) of the BioConductor open-source library (Gentleman et al., 2004). The raw data were then pre-processed using the GC-RMA variant (Wu et al., 2004) of the common RMA algorithm (Irizarry et al., 2003a), as implemented in the gcrma package of BioConductor (v2.6.0).
| Sample_platform_id | GPL341
| Sample_contact_name | Paul,C,Boutros
| Sample_contact_email | Paul.Boutros@utoronto.ca
| Sample_contact_institute | Ontario Institute for Cancer Research
| Sample_contact_address | 101 College Street, Suite 800
| Sample_contact_city | Toronto
| Sample_contact_state | Ontario
| Sample_contact_zip/postal_code | M5G 0A3
| Sample_contact_country | Canada
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234640/suppl/GSM234640.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234640/suppl/GSM234640.CHP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234640/suppl/GSM234640.DAT.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234640/suppl/GSM234640.EXP.gz
| Sample_series_id | GSE9226
| Sample_data_row_count | 15923
| |
|
GSM234641 | GPL341 |
|
SpragueDawley-liver-control-rep3
|
control rat liver
|
Strain:Sprague/Dawley, Age:10-12 weeks, Tissue: liver, Gender: Male
|
Gene expression data from control rat liver
|
Sample_geo_accession | GSM234641
| Sample_status | Public on Nov 24 2009
| Sample_submission_date | Oct 04 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | No treatments were given.
| Sample_growth_protocol_ch1 | Male Sprague Dawley (SD) rats between the ages of 10 and 12 weeks were obtained from the breeding colonies of the National Public Health Institute, Division of Environmental Health, Kuopio, Finland. Rats were kept in stainless steel wire-mesh cages with unlimited access to standard animal feed (R36, Ewos, Södertälje, Sweden) and tap water. Lights were on between 7:00 and 19:00. Ambient room temperature and humidity were maintained at 21.5 ± 1 ?C and 55 ± 10%, respectively.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Liver was harvested, sliced, snap-frozen and stored in liquid nitrogen until homogenization. Total RNA was extracted using RNeasy kits (Qiagen) according to the manufacturer’s instructions. DNase (Qiagen) was added to the RNeasy elution column as recommended by the manufacturer. RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyser.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The isolated RNA was then assayed on Affymetrix RAE230-2 arrays at The Centre for Applied Genomics at The Hospital for Sick Children (Toronto, Canada) following standard manufacturer's protocols. That is, a total of 1.5 µg of purified total RNA template was reverse-transcribed to generate double-stranded cDNA. Following second strand cDNA synthesis, biotin-labeled antisense cRNA was generated by in vitro transcription. Next, 15 µg of each generated cRNA preparation was fragmented and hybridized to an Affymetrix RAE230-2 oliogonucleotide array. Automated washing, staining and scanning was done according to the manufacturer's protocols.
| Sample_hyb_protocol | The isolated RNA was then assayed on Affymetrix RAE230-2 arrays at The Centre for Applied Genomics at The Hospital for Sick Children (Toronto, Canada) following standard manufacturer's protocols. That is, a total of 1.5 µg of purified total RNA template was reverse-transcribed to generate double-stranded cDNA. Following second strand cDNA synthesis, biotin-labeled antisense cRNA was generated by in vitro transcription. Next, 15 µg of each generated cRNA preparation was fragmented and hybridized to an Affymetrix RAE230-2 oliogonucleotide array. Automated washing, staining and scanning was done according to the manufacturer's protocols.
| Sample_scan_protocol | The isolated RNA was then assayed on Affymetrix RAE230-2 arrays at The Centre for Applied Genomics at The Hospital for Sick Children (Toronto, Canada) following standard manufacturer's protocols. That is, a total of 1.5 µg of purified total RNA template was reverse-transcribed to generate double-stranded cDNA. Following second strand cDNA synthesis, biotin-labeled antisense cRNA was generated by in vitro transcription. Next, 15 µg of each generated cRNA preparation was fragmented and hybridized to an Affymetrix RAE230-2 oliogonucleotide array. Automated washing, staining and scanning was done according to the manufacturer's protocols.
| Sample_data_processing | Affymetrix array data were loaded into the R statistical environment (v2.4.1) using the affy package (v1.12.2) of the BioConductor open-source library (Gentleman et al., 2004). The raw data were then pre-processed using the GC-RMA variant (Wu et al., 2004) of the common RMA algorithm (Irizarry et al., 2003a), as implemented in the gcrma package of BioConductor (v2.6.0).
| Sample_platform_id | GPL341
| Sample_contact_name | Paul,C,Boutros
| Sample_contact_email | Paul.Boutros@utoronto.ca
| Sample_contact_institute | Ontario Institute for Cancer Research
| Sample_contact_address | 101 College Street, Suite 800
| Sample_contact_city | Toronto
| Sample_contact_state | Ontario
| Sample_contact_zip/postal_code | M5G 0A3
| Sample_contact_country | Canada
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234641/suppl/GSM234641.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234641/suppl/GSM234641.CHP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234641/suppl/GSM234641.DAT.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234641/suppl/GSM234641.EXP.gz
| Sample_series_id | GSE9226
| Sample_data_row_count | 15923
| |
|
GSM234642 | GPL341 |
|
SpragueDawley-liver-control-rep4
|
control rat liver
|
Strain:Sprague/Dawley, Age:10-12 weeks, Tissue: liver, Gender: Male
|
Gene expression data from control rat liver
|
Sample_geo_accession | GSM234642
| Sample_status | Public on Nov 24 2009
| Sample_submission_date | Oct 04 2007
| Sample_last_update_date | Aug 14 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | No treatments were given.
| Sample_growth_protocol_ch1 | Male Sprague Dawley (SD) rats between the ages of 10 and 12 weeks were obtained from the breeding colonies of the National Public Health Institute, Division of Environmental Health, Kuopio, Finland. Rats were kept in stainless steel wire-mesh cages with unlimited access to standard animal feed (R36, Ewos, Södertälje, Sweden) and tap water. Lights were on between 7:00 and 19:00. Ambient room temperature and humidity were maintained at 21.5 ± 1 ?C and 55 ± 10%, respectively.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Liver was harvested, sliced, snap-frozen and stored in liquid nitrogen until homogenization. Total RNA was extracted using RNeasy kits (Qiagen) according to the manufacturer’s instructions. DNase (Qiagen) was added to the RNeasy elution column as recommended by the manufacturer. RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyser.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | The isolated RNA was then assayed on Affymetrix RAE230-2 arrays at The Centre for Applied Genomics at The Hospital for Sick Children (Toronto, Canada) following standard manufacturer's protocols. That is, a total of 1.5 µg of purified total RNA template was reverse-transcribed to generate double-stranded cDNA. Following second strand cDNA synthesis, biotin-labeled antisense cRNA was generated by in vitro transcription. Next, 15 µg of each generated cRNA preparation was fragmented and hybridized to an Affymetrix RAE230-2 oliogonucleotide array. Automated washing, staining and scanning was done according to the manufacturer's protocols.
| Sample_hyb_protocol | The isolated RNA was then assayed on Affymetrix RAE230-2 arrays at The Centre for Applied Genomics at The Hospital for Sick Children (Toronto, Canada) following standard manufacturer's protocols. That is, a total of 1.5 µg of purified total RNA template was reverse-transcribed to generate double-stranded cDNA. Following second strand cDNA synthesis, biotin-labeled antisense cRNA was generated by in vitro transcription. Next, 15 µg of each generated cRNA preparation was fragmented and hybridized to an Affymetrix RAE230-2 oliogonucleotide array. Automated washing, staining and scanning was done according to the manufacturer's protocols.
| Sample_scan_protocol | The isolated RNA was then assayed on Affymetrix RAE230-2 arrays at The Centre for Applied Genomics at The Hospital for Sick Children (Toronto, Canada) following standard manufacturer's protocols. That is, a total of 1.5 µg of purified total RNA template was reverse-transcribed to generate double-stranded cDNA. Following second strand cDNA synthesis, biotin-labeled antisense cRNA was generated by in vitro transcription. Next, 15 µg of each generated cRNA preparation was fragmented and hybridized to an Affymetrix RAE230-2 oliogonucleotide array. Automated washing, staining and scanning was done according to the manufacturer's protocols.
| Sample_data_processing | Affymetrix array data were loaded into the R statistical environment (v2.4.1) using the affy package (v1.12.2) of the BioConductor open-source library (Gentleman et al., 2004). The raw data were then pre-processed using the GC-RMA variant (Wu et al., 2004) of the common RMA algorithm (Irizarry et al., 2003a), as implemented in the gcrma package of BioConductor (v2.6.0).
| Sample_platform_id | GPL341
| Sample_contact_name | Paul,C,Boutros
| Sample_contact_email | Paul.Boutros@utoronto.ca
| Sample_contact_institute | Ontario Institute for Cancer Research
| Sample_contact_address | 101 College Street, Suite 800
| Sample_contact_city | Toronto
| Sample_contact_state | Ontario
| Sample_contact_zip/postal_code | M5G 0A3
| Sample_contact_country | Canada
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234642/suppl/GSM234642.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234642/suppl/GSM234642.CHP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234642/suppl/GSM234642.DAT.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM234nnn/GSM234642/suppl/GSM234642.EXP.gz
| Sample_series_id | GSE9226
| Sample_data_row_count | 15923
| |
|
|
|
Make groups for comparisons |
(2 groups will be compared at a time) |
|
Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|