Search results for the GEO ID: GSE6102  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM141501 | GPL85 |
|
Proximal colon casein 1
|
Rat Proximal colon
|
Male Sprague Dawley rat, 40 weeks post-AOM, life-time ingestion of casein based diet(CAS), proximal colon
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM141501
| | Sample_status | Public on Oct 26 2006
| | Sample_submission_date | Oct 23 2006
| | Sample_last_update_date | Oct 25 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from each of 7 animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
| | Sample_hyb_protocol | Ten ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat U34A GeneChip (3 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | To compare array data between GeneChips, we scaled the average of the fluorescent intensities of all probes on each array to a constant target intensity of 500.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Rijin,,Xiao
| | Sample_contact_email | xiaorijin@uams.edu
| | Sample_contact_phone | 501-364-2790
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_institute | Nutrition Center, Arkansas Chidren's Hospital
| | Sample_contact_address | 2020 Marshall Street
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141501/suppl/GSM141501.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141501/suppl/GSM141501.EXP.gz
| | Sample_series_id | GSE6102
| | Sample_data_row_count | 8799
| | |
|
GSM141502 | GPL85 |
|
Proximal colon casein 2
|
Rat Proximal colon
|
Male Sprague Dawley rat, 40 weeks post-AOM, life-time ingestion of casein based diet (CAS), proximal colon
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM141502
| | Sample_status | Public on Oct 26 2006
| | Sample_submission_date | Oct 23 2006
| | Sample_last_update_date | Oct 25 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from each of 7 animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
| | Sample_hyb_protocol | Ten ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat U34A GeneChip (3 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | To compare array data between GeneChips, we scaled the average of the fluorescent intensities of all probes on each array to a constant target intensity of 500.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Rijin,,Xiao
| | Sample_contact_email | xiaorijin@uams.edu
| | Sample_contact_phone | 501-364-2790
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_institute | Nutrition Center, Arkansas Chidren's Hospital
| | Sample_contact_address | 2020 Marshall Street
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141502/suppl/GSM141502.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141502/suppl/GSM141502.EXP.gz
| | Sample_series_id | GSE6102
| | Sample_data_row_count | 8799
| | |
|
GSM141503 | GPL85 |
|
Proximal colon casein 3
|
Rat Proximal colon
|
Male Sprague Dawley rat, 40 weeks post-AOM, life-time ingestion of casein based diet (CAS), proximal colon
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM141503
| | Sample_status | Public on Oct 26 2006
| | Sample_submission_date | Oct 23 2006
| | Sample_last_update_date | Oct 25 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from each of 7 animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
| | Sample_hyb_protocol | Ten ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat U34A GeneChip (3 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | To compare array data between GeneChips, we scaled the average of the fluorescent intensities of all probes on each array to a constant target intensity of 500.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Rijin,,Xiao
| | Sample_contact_email | xiaorijin@uams.edu
| | Sample_contact_phone | 501-364-2790
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_institute | Nutrition Center, Arkansas Chidren's Hospital
| | Sample_contact_address | 2020 Marshall Street
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141503/suppl/GSM141503.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141503/suppl/GSM141503.EXP.gz
| | Sample_series_id | GSE6102
| | Sample_data_row_count | 8799
| | |
|
GSM141504 | GPL85 |
|
Proximal colon soy 1
|
Rat Proximal colon
|
Male Sprague Dawley rat, 40 weeks post-AOM, life-time ingestion of casein based diet (CAS), proximal colon
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM141504
| | Sample_status | Public on Oct 26 2006
| | Sample_submission_date | Oct 23 2006
| | Sample_last_update_date | Oct 25 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from each of 7 animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
| | Sample_hyb_protocol | Ten ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat U34A GeneChip (3 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | To compare array data between GeneChips, we scaled the average of the fluorescent intensities of all probes on each array to a constant target intensity of 500.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Rijin,,Xiao
| | Sample_contact_email | xiaorijin@uams.edu
| | Sample_contact_phone | 501-364-2790
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_institute | Nutrition Center, Arkansas Chidren's Hospital
| | Sample_contact_address | 2020 Marshall Street
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141504/suppl/GSM141504.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141504/suppl/GSM141504.EXP.gz
| | Sample_series_id | GSE6102
| | Sample_data_row_count | 8799
| | |
|
GSM141505 | GPL85 |
|
Proximal colon soy 2
|
Rat Proximal colon
|
Male Sprague Dawley rat, 40 weeks post-AOM, life-time ingestion of casein based diet (CAS), proximal colon
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM141505
| | Sample_status | Public on Oct 26 2006
| | Sample_submission_date | Oct 23 2006
| | Sample_last_update_date | Oct 25 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from each of 7 animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
| | Sample_hyb_protocol | Ten ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat U34A GeneChip (3 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | To compare array data between GeneChips, we scaled the average of the fluorescent intensities of all probes on each array to a constant target intensity of 500.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Rijin,,Xiao
| | Sample_contact_email | xiaorijin@uams.edu
| | Sample_contact_phone | 501-364-2790
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_institute | Nutrition Center, Arkansas Chidren's Hospital
| | Sample_contact_address | 2020 Marshall Street
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141505/suppl/GSM141505.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141505/suppl/GSM141505.EXP.gz
| | Sample_series_id | GSE6102
| | Sample_data_row_count | 8799
| | |
|
GSM141506 | GPL85 |
|
Proximal colon soy 3
|
Rat Proximal colon
|
Male Sprague Dawley rat, 40 weeks post-AOM, life-time ingestion of casein based diet (CAS), proximal colon
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM141506
| | Sample_status | Public on Oct 26 2006
| | Sample_submission_date | Oct 23 2006
| | Sample_last_update_date | Oct 25 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from each of 7 animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
| | Sample_hyb_protocol | Ten ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat U34A GeneChip (3 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | To compare array data between GeneChips, we scaled the average of the fluorescent intensities of all probes on each array to a constant target intensity of 500.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Rijin,,Xiao
| | Sample_contact_email | xiaorijin@uams.edu
| | Sample_contact_phone | 501-364-2790
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_institute | Nutrition Center, Arkansas Chidren's Hospital
| | Sample_contact_address | 2020 Marshall Street
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141506/suppl/GSM141506.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141506/suppl/GSM141506.EXP.gz
| | Sample_series_id | GSE6102
| | Sample_data_row_count | 8799
| | |
|
GSM141507 | GPL85 |
|
Proximal colon whey 1
|
Rat Proximal colon
|
Male Sprague Dawley rat, 40 weeks post-AOM, life-time ingestion of casein based diet (CAS), proximal colon
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM141507
| | Sample_status | Public on Oct 26 2006
| | Sample_submission_date | Oct 23 2006
| | Sample_last_update_date | Oct 25 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from each of 7 animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
| | Sample_hyb_protocol | Ten ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat U34A GeneChip (3 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | To compare array data between GeneChips, we scaled the average of the fluorescent intensities of all probes on each array to a constant target intensity of 500.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Rijin,,Xiao
| | Sample_contact_email | xiaorijin@uams.edu
| | Sample_contact_phone | 501-364-2790
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_institute | Nutrition Center, Arkansas Chidren's Hospital
| | Sample_contact_address | 2020 Marshall Street
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141507/suppl/GSM141507.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141507/suppl/GSM141507.EXP.gz
| | Sample_series_id | GSE6102
| | Sample_data_row_count | 8799
| | |
|
GSM141508 | GPL85 |
|
Proximal colon whey 2
|
Rat Proximal colon
|
Male Sprague Dawley rat, 40 weeks post-AOM, life-time ingestion of casein based diet (CAS), proximal colon
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM141508
| | Sample_status | Public on Oct 26 2006
| | Sample_submission_date | Oct 23 2006
| | Sample_last_update_date | Oct 25 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from each of 7 animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
| | Sample_hyb_protocol | Ten ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat U34A GeneChip (3 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | To compare array data between GeneChips, we scaled the average of the fluorescent intensities of all probes on each array to a constant target intensity of 500.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Rijin,,Xiao
| | Sample_contact_email | xiaorijin@uams.edu
| | Sample_contact_phone | 501-364-2790
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_institute | Nutrition Center, Arkansas Chidren's Hospital
| | Sample_contact_address | 2020 Marshall Street
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141508/suppl/GSM141508.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141508/suppl/GSM141508.EXP.gz
| | Sample_series_id | GSE6102
| | Sample_data_row_count | 8799
| | |
|
GSM141509 | GPL85 |
|
Proximal colon whey 3
|
Rat Proximal colon
|
Male Sprague Dawley rat, 40 weeks post-AOM, life-time ingestion of casein based diet (CAS), proximal colon
|
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Sample_geo_accession | GSM141509
| | Sample_status | Public on Oct 26 2006
| | Sample_submission_date | Oct 23 2006
| | Sample_last_update_date | Oct 25 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Pooled RNA (equal amounts of RNA from each of 7 animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
| | Sample_hyb_protocol | Ten ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat U34A GeneChip (3 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
| | Sample_scan_protocol | GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
| | Sample_data_processing | To compare array data between GeneChips, we scaled the average of the fluorescent intensities of all probes on each array to a constant target intensity of 500.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Rijin,,Xiao
| | Sample_contact_email | xiaorijin@uams.edu
| | Sample_contact_phone | 501-364-2790
| | Sample_contact_fax | 501-364-3161
| | Sample_contact_institute | Nutrition Center, Arkansas Chidren's Hospital
| | Sample_contact_address | 2020 Marshall Street
| | Sample_contact_city | Little Rock
| | Sample_contact_state | AR
| | Sample_contact_zip/postal_code | 72202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141509/suppl/GSM141509.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM141nnn/GSM141509/suppl/GSM141509.EXP.gz
| | Sample_series_id | GSE6102
| | Sample_data_row_count | 8799
| | |
|
| |
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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