Search results for the GEO ID: GSE28447 |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM703135 | GPL1261 |
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Skeletal muscle, WT
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Skeletal muscle of control non-transgenic mice
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gender: female
strain: C57BL6
age: 4 months
genotype/variation: wildtype
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none
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Sample_geo_accession | GSM703135
| Sample_status | Public on Apr 08 2011
| Sample_submission_date | Apr 07 2011
| Sample_last_update_date | Apr 08 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted from the three animals using Trizol (WAKO).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 5µg of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Affymetrix). Double-stranded cDNA was cleaned up by using Phase Lock Gels (Eppendorf)-Phenol/Chloroform Extraction (Ambion). In vitro transcription was performed on all of cDNA using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
| Sample_hyb_protocol | 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.
| Sample_scan_protocol | Scanning was performed in an Affymetrix GeneChip scanner 3000. Chip analysis was performed using the Affymetrix GeneChip Operating Software v1.3.
| Sample_data_processing | Fluorescence intensity in the transgenic groups was normalized to that in the non-transgenic group by equating the overall fluorescence intensity for the entire chip of each group. The average values were scaled to 100 so that all chips could be directly compared.
| Sample_platform_id | GPL1261
| Sample_contact_name | Takako,,Takai
| Sample_contact_email | takai.com@mri.tmd.ac.jp
| Sample_contact_phone | +81-3-5803-4763
| Sample_contact_fax | +81-3-5803-0247
| Sample_contact_department | Bioinformatics
| Sample_contact_institute | Tokyo Medical and Dental University
| Sample_contact_address | 1-5-45 Yushima, Bunkyo-Ku
| Sample_contact_city | Tokyo
| Sample_contact_zip/postal_code | 113-8510
| Sample_contact_country | Japan
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM703nnn/GSM703135/suppl/GSM703135.CEL.gz
| Sample_series_id | GSE28447
| Sample_data_row_count | 45101
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GSM703136 | GPL1261 |
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Skeletal muscle, RXR-gamma TG
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Skeletal muscle of transgenic mice overexpressing RXR
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gender: female
strain: C57BL6
age: 4 months
genotype/variation: RXR-gamma
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none
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Sample_geo_accession | GSM703136
| Sample_status | Public on Apr 08 2011
| Sample_submission_date | Apr 07 2011
| Sample_last_update_date | Apr 08 2011
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | RXR-gamma was transgenically overexpressed in the skeletal muscle of mice.
| Sample_growth_protocol_ch1 | RXR-gamma mice, under the control of the human alpha-actin promoter, were allowed free access to food (CRF-1; Charles River) and water.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted from the three animals using Trizol (WAKO).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 5µg of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Affymetrix). Double-stranded cDNA was cleaned up by using Phase Lock Gels (Eppendorf)-Phenol/Chloroform Extraction (Ambion). In vitro transcription was performed on all of cDNA using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
| Sample_hyb_protocol | 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual. Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.
| Sample_scan_protocol | Scanning was performed in an Affymetrix GeneChip scanner 3000. Chip analysis was performed using the Affymetrix GeneChip Operating Software v1.3.
| Sample_data_processing | Fluorescence intensity in the transgenic groups was normalized to that in the non-transgenic group by equating the overall fluorescence intensity for the entire chip of each group. The average values were scaled to 100 so that all chips could be directly compared.
| Sample_platform_id | GPL1261
| Sample_contact_name | Takako,,Takai
| Sample_contact_email | takai.com@mri.tmd.ac.jp
| Sample_contact_phone | +81-3-5803-4763
| Sample_contact_fax | +81-3-5803-0247
| Sample_contact_department | Bioinformatics
| Sample_contact_institute | Tokyo Medical and Dental University
| Sample_contact_address | 1-5-45 Yushima, Bunkyo-Ku
| Sample_contact_city | Tokyo
| Sample_contact_zip/postal_code | 113-8510
| Sample_contact_country | Japan
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM703nnn/GSM703136/suppl/GSM703136.CEL.gz
| Sample_series_id | GSE28447
| Sample_data_row_count | 45101
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