Search results for the GEO ID: GSE7187 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM172899 | GPL339 |
|
Fiona Biological Replicate 1
|
Skeletal muscle tibialis anterior (TA) from fiona transgenic line
|
Male mice from fiona transgenic line (dystrophin-deficient with a transgene expressing high level of full length utrophin) were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction. Biological Replicate 1.
|
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
Sample_geo_accession | GSM172899
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Transgenic line fiona produced in house by over expressing utrophin on mdx (C57BL/10ScSn-Dmdmdx/J) backgound.Breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172899/suppl/GSM172899.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
| |
|
GSM172900 | GPL339 |
|
Fiona Biological Replicate2
|
Skeletal muscle tibialis anterior (TA) from fiona transgenic line
|
Male mice from fiona transgenic line (dystrophin-deficient with a transgene expressing high level of full length utrophin) were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
Sample_geo_accession | GSM172900
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Transgenic line fiona produced in house by over expressing utrophin on mdx (C57BL/10ScSn-Dmdmdx/J) backgound.Breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172900/suppl/GSM172900.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
| |
|
GSM172901 | GPL339 |
|
Fiona Biological Replicate3
|
Skeletal muscle tibialis anterior (TA) from fiona transgenic line
|
Male mice from fiona transgenic line (dystrophin-deficient with a transgene expressing high level of full length utrophin) were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
Sample_geo_accession | GSM172901
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Transgenic line fiona produced in house by over expressing utrophin on mdx (C57BL/10ScSn-Dmdmdx/J) backgound.Breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172901/suppl/GSM172901.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
| |
|
GSM172902 | GPL339 |
|
Fiona Biological Replicate 4
|
Skeletal muscle tibialis anterior (TA) from fiona transgenic line
|
Male mice from fiona transgenic line (dystrophin-deficient with a transgene expressing high level of full length utrophin) were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
Sample_geo_accession | GSM172902
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Transgenic line fiona produced in house by over expressing utrophin on mdx (C57BL/10ScSn-Dmdmdx/J) backgound.Breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172902/suppl/GSM172902.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
| |
|
GSM172903 | GPL339 |
|
Fiona Biological Replicate 5
|
Skeletal muscle tibialis anterior (TA) from fiona transgenic line
|
Male mice from fiona transgenic line (dystrophin-deficient with a transgene expressing high level of full length utrophin) were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
Sample_geo_accession | GSM172903
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Transgenic line fiona produced in house by over expressing utrophin on mdx (C57BL/10ScSn-Dmdmdx/J) backgound.Breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172903/suppl/GSM172903.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
| |
|
GSM172904 | GPL339 |
|
mdx Biological Replicate 1
|
Skeletal muscle tibialis anterior (TA) from mdx line
|
Male mice from mdx (C57BL/10ScSn-Dmdmdx/J) line were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
Sample_geo_accession | GSM172904
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | mdx (C57BL/10ScSn-Dmdmdx/J) breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172904/suppl/GSM172904.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
| |
|
GSM172905 | GPL339 |
|
mdx Biological Replicate 2
|
Skeletal muscle tibialis anterior (TA) from mdx line
|
Male mice from mdx (C57BL/10ScSn-Dmdmdx/J) line were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
Sample_geo_accession | GSM172905
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | mdx (C57BL/10ScSn-Dmdmdx/J) breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172905/suppl/GSM172905.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
| |
|
GSM172906 | GPL339 |
|
mdx Biological Replicate 3
|
Skeletal muscle tibialis anterior (TA) from mdx line
|
Male mice from mdx (C57BL/10ScSn-Dmdmdx/J) line were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
Sample_geo_accession | GSM172906
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | mdx (C57BL/10ScSn-Dmdmdx/J) breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172906/suppl/GSM172906.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
| |
|
GSM172907 | GPL339 |
|
mdx Biological Replicate 4
|
Skeletal muscle tibialis anterior (TA) from mdx line
|
Male mice from mdx (C57BL/10ScSn-Dmdmdx/J) line were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
Sample_geo_accession | GSM172907
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | mdx (C57BL/10ScSn-Dmdmdx/J) breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172907/suppl/GSM172907.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
| |
|
GSM172908 | GPL339 |
|
mdx Biological Replicate 5
|
Skeletal muscle tibialis anterior (TA) from mdx line
|
Male mice from mdx (C57BL/10ScSn-Dmdmdx/J) line were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
Sample_geo_accession | GSM172908
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | mdx (C57BL/10ScSn-Dmdmdx/J) breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172908/suppl/GSM172908.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
| |
|
GSM172909 | GPL339 |
|
mdx Biological Replicate 6
|
Skeletal muscle tibialis anterior (TA) from mdx line
|
Male mice from mdx (C57BL/10ScSn-Dmdmdx/J) line were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
Sample_geo_accession | GSM172909
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | mdx (C57BL/10ScSn-Dmdmdx/J) breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172909/suppl/GSM172909.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
| |
|
GSM172910 | GPL339 |
|
Normal Biological Replicate 1
|
Skeletal muscle tibialis anterior (TA) from Normal wild-type mice
|
Male wild-type (C57BL/10SnJ) mice were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
Sample_geo_accession | GSM172910
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Normal wild-type (C57BL/10SnJ) breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172910/suppl/GSM172910.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
| |
|
GSM172911 | GPL339 |
|
Normal Biological Replicate 2
|
Skeletal muscle tibialis anterior (TA) from Normal wild-type mice
|
Male wild-type (C57BL/10SnJ) mice were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
Sample_geo_accession | GSM172911
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Normal wild-type (C57BL/10SnJ) breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172911/suppl/GSM172911.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
| |
|
GSM172912 | GPL339 |
|
Normal Biological Replicate 3
|
Skeletal muscle tibialis anterior (TA) from Normal wild-type mice
|
Male wild-type (C57BL/10SnJ) mice were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
Sample_geo_accession | GSM172912
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Normal wild-type (C57BL/10SnJ) breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172912/suppl/GSM172912.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
| |
|
GSM172913 | GPL339 |
|
Normal Biological Replicate 4
|
Skeletal muscle tibialis anterior (TA) from Normal wild-type mice
|
Male wild-type (C57BL/10SnJ) mice were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
Sample_geo_accession | GSM172913
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Normal wild-type (C57BL/10SnJ) breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172913/suppl/GSM172913.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
| |
|
GSM172914 | GPL339 |
|
Normal Biological Replicate 5
|
Skeletal muscle tibialis anterior (TA) from Normal wild-type mice
|
Male wild-type (C57BL/10SnJ) mice were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
Sample_geo_accession | GSM172914
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Normal wild-type (C57BL/10SnJ) breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172914/suppl/GSM172914.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
| |
|
GSM172915 | GPL339 |
|
Normal Biological Replicate 6
|
Skeletal muscle tibialis anterior (TA) from Normal wild-type mice
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Male wild-type (C57BL/10SnJ) mice were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
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Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
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Sample_geo_accession | GSM172915
| Sample_status | Public on Apr 23 2008
| Sample_submission_date | Mar 05 2007
| Sample_last_update_date | Apr 23 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_biomaterial_provider_ch1 | Normal wild-type (C57BL/10SnJ) breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
| Sample_growth_protocol_ch1 | male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | 8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
| Sample_hyb_protocol | Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
| Sample_scan_protocol | Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
| Sample_data_processing | We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
| Sample_platform_id | GPL339
| Sample_contact_name | Dilair,,Baban
| Sample_contact_email | dilair.baban@well.ox.ac.uk
| Sample_contact_phone | +44(0)1865287521
| Sample_contact_fax | +44(0)1865287501
| Sample_contact_laboratory | Genomics
| Sample_contact_department | Wellcome Trust Centre Human Genetics
| Sample_contact_institute | University of Oxford
| Sample_contact_address | Roosevelt Drive
| Sample_contact_city | Oxford
| Sample_contact_zip/postal_code | OX3 7BN
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM172nnn/GSM172915/suppl/GSM172915.CEL.gz
| Sample_series_id | GSE7187
| Sample_data_row_count | 22690
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