Search results for the GEO ID: GSE13436  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM338411 | GPL1355 |
|
EOM-hyperthyroid-R1
|
extraocular muscles, dissected, fresh
|
Strain: Sprague-Dawley
Age category: adult
|
In general, recommendations by Affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2).
|
| Sample_geo_accession | GSM338411
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Mar 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 25 ug T3 per 100 g body weight, administered every second day by intraperitoneal injections for six weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.
| | Sample_hyb_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.
| | Sample_scan_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.
| | Sample_data_processing | Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Thomas,S,Postler
| | Sample_contact_email | postler@fas.harvard.edu
| | Sample_contact_phone | 5087861491
| | Sample_contact_laboratory | Rubinstein Lab
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 421 Curie Boulevard
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338411/suppl/GSM338411.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338411/suppl/GSM338411.CHP.gz
| | Sample_series_id | GSE13414
| | Sample_series_id | GSE13436
| | Sample_data_row_count | 31099
| | |
|
GSM338414 | GPL1355 |
|
EOM-hyperthyroid-R3
|
extraocular muscles, dissected, fresh
|
Strain: Sprague-Dawley
Age category: adult
|
In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)
|
| Sample_geo_accession | GSM338414
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Mar 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 25 ug T3 per 100 g body weight, administered every second day by intraperitoneal injections for six weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.
| | Sample_hyb_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.
| | Sample_scan_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.
| | Sample_data_processing | Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Thomas,S,Postler
| | Sample_contact_email | postler@fas.harvard.edu
| | Sample_contact_phone | 5087861491
| | Sample_contact_laboratory | Rubinstein Lab
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 421 Curie Boulevard
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338414/suppl/GSM338414.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338414/suppl/GSM338414.CHP.gz
| | Sample_series_id | GSE13414
| | Sample_series_id | GSE13436
| | Sample_data_row_count | 31099
| | |
|
GSM338415 | GPL1355 |
|
EOM-hyperthyroid-R5
|
extraocular muscles, dissected, fresh
|
Strain: Sprague-Dawley
Age category: adult
|
In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)
|
| Sample_geo_accession | GSM338415
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Mar 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 25 ug T3 per 100 g body weight, administered every second day by intraperitoneal injections for six weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.
| | Sample_hyb_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.
| | Sample_scan_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.
| | Sample_data_processing | Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Thomas,S,Postler
| | Sample_contact_email | postler@fas.harvard.edu
| | Sample_contact_phone | 5087861491
| | Sample_contact_laboratory | Rubinstein Lab
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 421 Curie Boulevard
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338415/suppl/GSM338415.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338415/suppl/GSM338415.CHP.gz
| | Sample_series_id | GSE13414
| | Sample_series_id | GSE13436
| | Sample_data_row_count | 31099
| | |
|
GSM338416 | GPL1355 |
|
EOM-hyperthyroid-R2
|
extraocular muscles, dissected, fresh
|
Strain: Sprague-Dawley
Age category: adult
|
In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)
|
| Sample_geo_accession | GSM338416
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Mar 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 25 ug T3 per 100 g body weight, administered every second day by intraperitoneal injections for six weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.
| | Sample_hyb_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.
| | Sample_scan_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.
| | Sample_data_processing | Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Thomas,S,Postler
| | Sample_contact_email | postler@fas.harvard.edu
| | Sample_contact_phone | 5087861491
| | Sample_contact_laboratory | Rubinstein Lab
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 421 Curie Boulevard
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338416/suppl/GSM338416.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338416/suppl/GSM338416.CHP.gz
| | Sample_series_id | GSE13414
| | Sample_series_id | GSE13436
| | Sample_data_row_count | 31099
| | |
|
GSM338417 | GPL1355 |
|
EOM-control-R7
|
extraocular muscles, dissected, fresh
|
Strain: Sprague-Dawley
Age category: adult
|
In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)
|
| Sample_geo_accession | GSM338417
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Mar 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Untreated control
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.
| | Sample_hyb_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.
| | Sample_scan_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.
| | Sample_data_processing | Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Thomas,S,Postler
| | Sample_contact_email | postler@fas.harvard.edu
| | Sample_contact_phone | 5087861491
| | Sample_contact_laboratory | Rubinstein Lab
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 421 Curie Boulevard
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338417/suppl/GSM338417.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338417/suppl/GSM338417.CHP.gz
| | Sample_series_id | GSE13414
| | Sample_series_id | GSE13436
| | Sample_data_row_count | 31099
| | |
|
GSM338418 | GPL1355 |
|
EOM-control-R8
|
extraocular muscles, dissected, fresh
|
Strain: Sprague-Dawley
Age category: adult
|
In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)
|
| Sample_geo_accession | GSM338418
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Mar 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Untreated control
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.
| | Sample_hyb_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.
| | Sample_scan_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.
| | Sample_data_processing | Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Thomas,S,Postler
| | Sample_contact_email | postler@fas.harvard.edu
| | Sample_contact_phone | 5087861491
| | Sample_contact_laboratory | Rubinstein Lab
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 421 Curie Boulevard
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338418/suppl/GSM338418.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338418/suppl/GSM338418.CHP.gz
| | Sample_series_id | GSE13414
| | Sample_series_id | GSE13436
| | Sample_data_row_count | 31099
| | |
|
GSM338419 | GPL1355 |
|
EOM-control-R9
|
extraocular muscles, dissected, fresh
|
Strain: Sprague-Dawley
Age category: adult
|
In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)
|
| Sample_geo_accession | GSM338419
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Mar 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Untreated control
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.
| | Sample_hyb_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.
| | Sample_scan_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.
| | Sample_data_processing | Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Thomas,S,Postler
| | Sample_contact_email | postler@fas.harvard.edu
| | Sample_contact_phone | 5087861491
| | Sample_contact_laboratory | Rubinstein Lab
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 421 Curie Boulevard
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338419/suppl/GSM338419.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338419/suppl/GSM338419.CHP.gz
| | Sample_series_id | GSE13414
| | Sample_series_id | GSE13436
| | Sample_data_row_count | 31099
| | |
|
GSM338420 | GPL1355 |
|
EOM-control-R11
|
extraocular muscles, dissected, fresh
|
Strain: Sprague-Dawley
Age category: adult
|
In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)
|
| Sample_geo_accession | GSM338420
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Mar 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Untreated control
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.
| | Sample_hyb_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.
| | Sample_scan_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.
| | Sample_data_processing | Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Thomas,S,Postler
| | Sample_contact_email | postler@fas.harvard.edu
| | Sample_contact_phone | 5087861491
| | Sample_contact_laboratory | Rubinstein Lab
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 421 Curie Boulevard
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338420/suppl/GSM338420.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338420/suppl/GSM338420.CHP.gz
| | Sample_series_id | GSE13414
| | Sample_series_id | GSE13436
| | Sample_data_row_count | 31099
| | |
|
GSM338421 | GPL1355 |
|
TA-hyperthyroid-R1
|
tibialis anterior, dissected, fresh
|
Strain: Sprague-Dawley
Age category: adult
|
In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)
|
| Sample_geo_accession | GSM338421
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Mar 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 25 ug T3 per 100 g body weight, administered every second day by intraperitoneal injections for six weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.
| | Sample_hyb_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.
| | Sample_scan_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.
| | Sample_data_processing | Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Thomas,S,Postler
| | Sample_contact_email | postler@fas.harvard.edu
| | Sample_contact_phone | 5087861491
| | Sample_contact_laboratory | Rubinstein Lab
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 421 Curie Boulevard
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338421/suppl/GSM338421.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338421/suppl/GSM338421.CHP.gz
| | Sample_series_id | GSE13413
| | Sample_series_id | GSE13436
| | Sample_data_row_count | 31099
| | |
|
GSM338422 | GPL1355 |
|
TA-hyperthyroid-R3
|
tibialis anterior, dissected, fresh
|
Strain: Sprague-Dawley
Age category: adult
|
In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)
|
| Sample_geo_accession | GSM338422
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Mar 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 25 ug T3 per 100 g body weight, administered every second day by intraperitoneal injections for six weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.
| | Sample_hyb_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.
| | Sample_scan_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.
| | Sample_data_processing | Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Thomas,S,Postler
| | Sample_contact_email | postler@fas.harvard.edu
| | Sample_contact_phone | 5087861491
| | Sample_contact_laboratory | Rubinstein Lab
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 421 Curie Boulevard
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338422/suppl/GSM338422.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338422/suppl/GSM338422.CHP.gz
| | Sample_series_id | GSE13413
| | Sample_series_id | GSE13436
| | Sample_data_row_count | 31099
| | |
|
GSM338423 | GPL1355 |
|
TA-hyperthyroid-R5
|
tibialis anterior, dissected, fresh
|
Strain: Sprague-Dawley
Age category: adult
|
In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)
|
| Sample_geo_accession | GSM338423
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Mar 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 25 ug T3 per 100 g body weight, administered every second day by intraperitoneal injections for six weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.
| | Sample_hyb_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.
| | Sample_scan_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.
| | Sample_data_processing | Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Thomas,S,Postler
| | Sample_contact_email | postler@fas.harvard.edu
| | Sample_contact_phone | 5087861491
| | Sample_contact_laboratory | Rubinstein Lab
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 421 Curie Boulevard
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338423/suppl/GSM338423.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338423/suppl/GSM338423.CHP.gz
| | Sample_series_id | GSE13413
| | Sample_series_id | GSE13436
| | Sample_data_row_count | 31099
| | |
|
GSM338424 | GPL1355 |
|
TA-hyperthyroid-R2
|
tibialis anterior, dissected, fresh
|
Strain: Sprague-Dawley
Age category: adult
|
In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)
|
| Sample_geo_accession | GSM338424
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Mar 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | 25 ug T3 per 100 g body weight, administered every second day by intraperitoneal injections for six weeks
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.
| | Sample_hyb_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.
| | Sample_scan_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.
| | Sample_data_processing | Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Thomas,S,Postler
| | Sample_contact_email | postler@fas.harvard.edu
| | Sample_contact_phone | 5087861491
| | Sample_contact_laboratory | Rubinstein Lab
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 421 Curie Boulevard
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338424/suppl/GSM338424.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338424/suppl/GSM338424.CHP.gz
| | Sample_series_id | GSE13413
| | Sample_series_id | GSE13436
| | Sample_data_row_count | 31099
| | |
|
GSM338425 | GPL1355 |
|
TA-control-R7
|
tibialis anterior, dissected, fresh
|
Strain: Sprague-Dawley
Age category: adult
|
In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)
|
| Sample_geo_accession | GSM338425
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Mar 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Untreated control
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.
| | Sample_hyb_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.
| | Sample_scan_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.
| | Sample_data_processing | Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Thomas,S,Postler
| | Sample_contact_email | postler@fas.harvard.edu
| | Sample_contact_phone | 5087861491
| | Sample_contact_laboratory | Rubinstein Lab
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 421 Curie Boulevard
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338425/suppl/GSM338425.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338425/suppl/GSM338425.CHP.gz
| | Sample_series_id | GSE13413
| | Sample_series_id | GSE13436
| | Sample_data_row_count | 31099
| | |
|
GSM338426 | GPL1355 |
|
TA-control-R8
|
tibialis anterior, dissected, fresh
|
Strain: Sprague-Dawley
Age category: adult
|
In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)
|
| Sample_geo_accession | GSM338426
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Mar 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Untreated control
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.
| | Sample_hyb_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.
| | Sample_scan_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.
| | Sample_data_processing | Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Thomas,S,Postler
| | Sample_contact_email | postler@fas.harvard.edu
| | Sample_contact_phone | 5087861491
| | Sample_contact_laboratory | Rubinstein Lab
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 421 Curie Boulevard
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338426/suppl/GSM338426.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338426/suppl/GSM338426.CHP.gz
| | Sample_series_id | GSE13413
| | Sample_series_id | GSE13436
| | Sample_data_row_count | 31099
| | |
|
GSM338427 | GPL1355 |
|
TA-control-R9
|
tibialis anterior, dissected, fresh
|
Strain: Sprague-Dawley
Age category: adult
|
In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)
|
| Sample_geo_accession | GSM338427
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Mar 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Untreated control
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.
| | Sample_hyb_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.
| | Sample_scan_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.
| | Sample_data_processing | Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Thomas,S,Postler
| | Sample_contact_email | postler@fas.harvard.edu
| | Sample_contact_phone | 5087861491
| | Sample_contact_laboratory | Rubinstein Lab
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 421 Curie Boulevard
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338427/suppl/GSM338427.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338427/suppl/GSM338427.CHP.gz
| | Sample_series_id | GSE13413
| | Sample_series_id | GSE13436
| | Sample_data_row_count | 31099
| | |
|
GSM338428 | GPL1355 |
|
TA-control-R11
|
tibialis anterior, dissected, fresh
|
Strain: Sprague-Dawley
Age category: adult
|
In general, recommendations by affymetrix were followed, as described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2)
|
| Sample_geo_accession | GSM338428
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Oct 30 2008
| | Sample_last_update_date | Mar 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Untreated control
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated using TRIzol Reagent (Invitrogen) and purified with RNeasy Mini or Micro Kit (Qiagen), as recommended by manufacturers. SUPERase-IN RNase inhibitor (Ambion) was added to samples in final concentration of 1 U/ul. Stored at -80 degC.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1 ug total RNA was transcribed to ss-cDNA using T7-Oligo(dT) Promoter and Superscript II Reverse Transcriptase. Subsequently, the second strand was confected using DNA Polymerase I (E. coli), in combination with RNA digestion by RNase H. Unincorporated nucleotides were removed by cDNA Cleanup Spin Columns. Finally, cDNA was transcribed in vitro to complementary RNA (cRNA) using T7 RNA Polymerase and NTPs mixed with biotinylated nucleotide analog. Proteins and unincorporated nucleotides were removed by cRNA Cleanup Spin Columns.
| | Sample_hyb_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 72 - 94.
| | Sample_scan_protocol | As described in Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 702232 Rev. 2), pages 95 - 97.
| | Sample_data_processing | Fluorescence was recorded using a GCS3000 laser scanner (Affymetrix) and analyzed with GeneChip Operating Software (GCOS) 1.4 (Affymetrix). Average signal intensities of the arrays were scaled to a default Target Signal Value of 150. No normalization procedure was applied.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Thomas,S,Postler
| | Sample_contact_email | postler@fas.harvard.edu
| | Sample_contact_phone | 5087861491
| | Sample_contact_laboratory | Rubinstein Lab
| | Sample_contact_department | Cell and Developmental Biology
| | Sample_contact_institute | University of Pennsylvania
| | Sample_contact_address | 421 Curie Boulevard
| | Sample_contact_city | Philadelphia
| | Sample_contact_state | PA
| | Sample_contact_zip/postal_code | 19104
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338428/suppl/GSM338428.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338428/suppl/GSM338428.CHP.gz
| | Sample_series_id | GSE13413
| | Sample_series_id | GSE13436
| | Sample_data_row_count | 31099
| | |
|
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Make groups for comparisons |
(2 groups will be compared at a time) |
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