Search results for the GEO ID: GSE22381  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM556778 | GPL1261 |
|
E10_otic_vesicle_wt_replicate1
|
Mouse otic vesicle at E10 wt
|
tissue: inner ear
genotype/variation: Wild-type
age: E10
|
Otic vesicle at E10, replicate1
|
| Sample_geo_accession | GSM556778
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jun 16 2010
| | Sample_last_update_date | Oct 04 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Otic vesicles were directly transferred into 1ml of TRIZOL. The 2B1 cell line was allowed to proliferate at 32oC in the presence of gamma-interferon to a confluency of 70-80% and then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_growth_protocol_ch1 | Otic vesicles from wild-type and Dlx5-null embryos were microdissected from mouse developmental stages E10 and E10.5 in ice-cold PBS (calcium and magnesium free). These were timed-pregnancies determined by a vaginal plug, and each embryo was staged independently in a litter by the number of somites. Once the vesicles were isolated as cleanly as possible from the embryos, they were placed in 1mg/ml solution of dispase dissolved in PBS (calcium and magnesium free) for 10-15 minutes on ice to facilitate the removal of closely attached mesenchyme. For each stage and genotype two biological replicates were collected, each comprising between 4 and 8 otic vesicles. For the 2B1 cell line, two independent cultures were used for both the empty vector-transfected and the Dlx5- transfected samples. Cells were grown in chick embryo fibroblast medium at 32oC to a confluency of 70-80% in the presence of gamma-interferon, then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | To synthesize biotin-labeled target (cRNA) for hybridization to Affymetrix arrays, 22ul of the purified cDNA were used as template in in-vitro transcription reactions using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, NY). Besides the template cDNA, all other components were added following the instructions provided by the manufacturer, and reactions were incubated at 37oC for 10 hours on the PCR machine mentioned above under 'extract protocol'. Labeled cRNA was purified using an RNA purification kit (Qiagen) following the manufacturer’s instructions and eluted in 50ul of water.
| | Sample_hyb_protocol | Fragmentation of cRNA was carried out following the standard Affymetrix procedure, and 10ug of fragmented cRNA from each sample was hybridized to the Mouse Genome 430 2.0 gene chips for 16-18 hours at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000.
| | Sample_data_processing | Analysis was carried out in Expression Console software (Affymetrix) by employing the Robust Multichip Analysis (RMA) algorithm. All normalized (log-base-2) expression values below 5.5 were considered ‘Absent’. For cell line microarray data the cut-off for making ‘Present’ calls was set to 4.8 since this was the expression of Dlx5 in Dlx5-transfected cells.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Samin,,Sajan
| | Sample_contact_institute | University of Chicago
| | Sample_contact_address | 920 E. 58th Street, CLSC 317
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60637
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556778/suppl/GSM556778.CEL.gz
| | Sample_series_id | GSE22381
| | Sample_data_row_count | 45101
| | |
|
GSM556779 | GPL1261 |
|
E10_otic_vesicle_wt_replicate2
|
Mouse otic vesicle at E10 wt
|
tissue: inner ear
genotype/variation: Wild-type
age: E10
|
Otic vesicle at E10, replicate2
|
| Sample_geo_accession | GSM556779
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jun 16 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Otic vesicles were directly transferred into 1ml of TRIZOL. The 2B1 cell line was allowed to proliferate at 32oC in the presence of gamma-interferon to a confluency of 70-80% and then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_growth_protocol_ch1 | Otic vesicles from wild-type and Dlx5-null embryos were microdissected from mouse developmental stages E10 and E10.5 in ice-cold PBS (calcium and magnesium free). These were timed-pregnancies determined by a vaginal plug, and each embryo was staged independently in a litter by the number of somites. Once the vesicles were isolated as cleanly as possible from the embryos, they were placed in 1mg/ml solution of dispase dissolved in PBS (calcium and magnesium free) for 10-15 minutes on ice to facilitate the removal of closely attached mesenchyme. For each stage and genotype two biological replicates were collected, each comprising between 4 and 8 otic vesicles. For the 2B1 cell line, two independent cultures were used for both the empty vector-transfected and the Dlx5- transfected samples. Cells were grown in chick embryo fibroblast medium at 32oC to a confluency of 70-80% in the presence of gamma-interferon, then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | To synthesize biotin-labeled target (cRNA) for hybridization to Affymetrix arrays, 22ul of the purified cDNA were used as template in in-vitro transcription reactions using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, NY). Besides the template cDNA, all other components were added following the instructions provided by the manufacturer, and reactions were incubated at 37oC for 10 hours on the PCR machine mentioned above under 'extract protocol'. Labeled cRNA was purified using an RNA purification kit (Qiagen) following the manufacturer’s instructions and eluted in 50ul of water.
| | Sample_hyb_protocol | Fragmentation of cRNA was carried out following the standard Affymetrix procedure, and 10ug of fragmented cRNA from each sample was hybridized to the Mouse Genome 430 2.0 gene chips for 16-18 hours at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000.
| | Sample_data_processing | Analysis was carried out in Expression Console software (Affymetrix) by employing the Robust Multichip Analysis (RMA) algorithm. All normalized (log-base-2) expression values below 5.5 were considered ‘Absent’. For cell line microarray data the cut-off for making ‘Present’ calls was set to 4.8 since this was the expression of Dlx5 in Dlx5-transfected cells.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Samin,,Sajan
| | Sample_contact_institute | University of Chicago
| | Sample_contact_address | 920 E. 58th Street, CLSC 317
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60637
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556779/suppl/GSM556779.CEL.gz
| | Sample_series_id | GSE22381
| | Sample_data_row_count | 45101
| | |
|
GSM556780 | GPL1261 |
|
E10_otic_vesicle_mut_replicate1
|
Mouse otic vesicle at E10 mut
|
tissue: inner ear
genotype/variation: Dlx5-null
age: E10
|
Otic vesicle at E10, replicate1
|
| Sample_geo_accession | GSM556780
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jun 16 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Otic vesicles were directly transferred into 1ml of TRIZOL. The 2B1 cell line was allowed to proliferate at 32oC in the presence of gamma-interferon to a confluency of 70-80% and then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_growth_protocol_ch1 | Otic vesicles from wild-type and Dlx5-null embryos were microdissected from mouse developmental stages E10 and E10.5 in ice-cold PBS (calcium and magnesium free). These were timed-pregnancies determined by a vaginal plug, and each embryo was staged independently in a litter by the number of somites. Once the vesicles were isolated as cleanly as possible from the embryos, they were placed in 1mg/ml solution of dispase dissolved in PBS (calcium and magnesium free) for 10-15 minutes on ice to facilitate the removal of closely attached mesenchyme. For each stage and genotype two biological replicates were collected, each comprising between 4 and 8 otic vesicles. For the 2B1 cell line, two independent cultures were used for both the empty vector-transfected and the Dlx5- transfected samples. Cells were grown in chick embryo fibroblast medium at 32oC to a confluency of 70-80% in the presence of gamma-interferon, then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | To synthesize biotin-labeled target (cRNA) for hybridization to Affymetrix arrays, 22ul of the purified cDNA were used as template in in-vitro transcription reactions using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, NY). Besides the template cDNA, all other components were added following the instructions provided by the manufacturer, and reactions were incubated at 37oC for 10 hours on the PCR machine mentioned above under 'extract protocol'. Labeled cRNA was purified using an RNA purification kit (Qiagen) following the manufacturer’s instructions and eluted in 50ul of water.
| | Sample_hyb_protocol | Fragmentation of cRNA was carried out following the standard Affymetrix procedure, and 10ug of fragmented cRNA from each sample was hybridized to the Mouse Genome 430 2.0 gene chips for 16-18 hours at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000.
| | Sample_data_processing | Analysis was carried out in Expression Console software (Affymetrix) by employing the Robust Multichip Analysis (RMA) algorithm. All normalized (log-base-2) expression values below 5.5 were considered ‘Absent’. For cell line microarray data the cut-off for making ‘Present’ calls was set to 4.8 since this was the expression of Dlx5 in Dlx5-transfected cells.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Samin,,Sajan
| | Sample_contact_institute | University of Chicago
| | Sample_contact_address | 920 E. 58th Street, CLSC 317
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60637
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556780/suppl/GSM556780.CEL.gz
| | Sample_series_id | GSE22381
| | Sample_data_row_count | 45101
| | |
|
GSM556781 | GPL1261 |
|
E10_otic_vesicle_mut_replicate2
|
Mouse otic vesicle at E10 mut
|
tissue: inner ear
genotype/variation: Dlx5-null
age: E10
|
Otic vesicle at E10, replicate2
|
| Sample_geo_accession | GSM556781
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jun 16 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Otic vesicles were directly transferred into 1ml of TRIZOL. The 2B1 cell line was allowed to proliferate at 32oC in the presence of gamma-interferon to a confluency of 70-80% and then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_growth_protocol_ch1 | Otic vesicles from wild-type and Dlx5-null embryos were microdissected from mouse developmental stages E10 and E10.5 in ice-cold PBS (calcium and magnesium free). These were timed-pregnancies determined by a vaginal plug, and each embryo was staged independently in a litter by the number of somites. Once the vesicles were isolated as cleanly as possible from the embryos, they were placed in 1mg/ml solution of dispase dissolved in PBS (calcium and magnesium free) for 10-15 minutes on ice to facilitate the removal of closely attached mesenchyme. For each stage and genotype two biological replicates were collected, each comprising between 4 and 8 otic vesicles. For the 2B1 cell line, two independent cultures were used for both the empty vector-transfected and the Dlx5- transfected samples. Cells were grown in chick embryo fibroblast medium at 32oC to a confluency of 70-80% in the presence of gamma-interferon, then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | To synthesize biotin-labeled target (cRNA) for hybridization to Affymetrix arrays, 22ul of the purified cDNA were used as template in in-vitro transcription reactions using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, NY). Besides the template cDNA, all other components were added following the instructions provided by the manufacturer, and reactions were incubated at 37oC for 10 hours on the PCR machine mentioned above under 'extract protocol'. Labeled cRNA was purified using an RNA purification kit (Qiagen) following the manufacturer’s instructions and eluted in 50ul of water.
| | Sample_hyb_protocol | Fragmentation of cRNA was carried out following the standard Affymetrix procedure, and 10ug of fragmented cRNA from each sample was hybridized to the Mouse Genome 430 2.0 gene chips for 16-18 hours at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000.
| | Sample_data_processing | Analysis was carried out in Expression Console software (Affymetrix) by employing the Robust Multichip Analysis (RMA) algorithm. All normalized (log-base-2) expression values below 5.5 were considered ‘Absent’. For cell line microarray data the cut-off for making ‘Present’ calls was set to 4.8 since this was the expression of Dlx5 in Dlx5-transfected cells.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Samin,,Sajan
| | Sample_contact_institute | University of Chicago
| | Sample_contact_address | 920 E. 58th Street, CLSC 317
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60637
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556781/suppl/GSM556781.CEL.gz
| | Sample_series_id | GSE22381
| | Sample_data_row_count | 45101
| | |
|
GSM556782 | GPL1261 |
|
E10.5_otic_vesicle_wt_replicate1
|
Mouse otic vesicle at E10.5 wt
|
tissue: inner ear
genotype/variation: Wild-type
age: E10.5
|
Otic vesicle at E10.5, replicate1
|
| Sample_geo_accession | GSM556782
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jun 16 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Otic vesicles were directly transferred into 1ml of TRIZOL. The 2B1 cell line was allowed to proliferate at 32oC in the presence of gamma-interferon to a confluency of 70-80% and then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_growth_protocol_ch1 | Otic vesicles from wild-type and Dlx5-null embryos were microdissected from mouse developmental stages E10 and E10.5 in ice-cold PBS (calcium and magnesium free). These were timed-pregnancies determined by a vaginal plug, and each embryo was staged independently in a litter by the number of somites. Once the vesicles were isolated as cleanly as possible from the embryos, they were placed in 1mg/ml solution of dispase dissolved in PBS (calcium and magnesium free) for 10-15 minutes on ice to facilitate the removal of closely attached mesenchyme. For each stage and genotype two biological replicates were collected, each comprising between 4 and 8 otic vesicles. For the 2B1 cell line, two independent cultures were used for both the empty vector-transfected and the Dlx5- transfected samples. Cells were grown in chick embryo fibroblast medium at 32oC to a confluency of 70-80% in the presence of gamma-interferon, then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | To synthesize biotin-labeled target (cRNA) for hybridization to Affymetrix arrays, 22ul of the purified cDNA were used as template in in-vitro transcription reactions using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, NY). Besides the template cDNA, all other components were added following the instructions provided by the manufacturer, and reactions were incubated at 37oC for 10 hours on the PCR machine mentioned above under 'extract protocol'. Labeled cRNA was purified using an RNA purification kit (Qiagen) following the manufacturer’s instructions and eluted in 50ul of water.
| | Sample_hyb_protocol | Fragmentation of cRNA was carried out following the standard Affymetrix procedure, and 10ug of fragmented cRNA from each sample was hybridized to the Mouse Genome 430 2.0 gene chips for 16-18 hours at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000.
| | Sample_data_processing | Analysis was carried out in Expression Console software (Affymetrix) by employing the Robust Multichip Analysis (RMA) algorithm. All normalized (log-base-2) expression values below 5.5 were considered ‘Absent’. For cell line microarray data the cut-off for making ‘Present’ calls was set to 4.8 since this was the expression of Dlx5 in Dlx5-transfected cells.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Samin,,Sajan
| | Sample_contact_institute | University of Chicago
| | Sample_contact_address | 920 E. 58th Street, CLSC 317
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60637
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556782/suppl/GSM556782.CEL.gz
| | Sample_series_id | GSE22381
| | Sample_data_row_count | 45101
| | |
|
GSM556783 | GPL1261 |
|
E10.5_otic_vesicle_wt_replicate2
|
Mouse otic vesicle at E10.5 wt
|
tissue: inner ear
genotype/variation: Wild-type
age: E10.5
|
Otic vesicle at E10.5, replicate1
|
| Sample_geo_accession | GSM556783
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jun 16 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Otic vesicles were directly transferred into 1ml of TRIZOL. The 2B1 cell line was allowed to proliferate at 32oC in the presence of gamma-interferon to a confluency of 70-80% and then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_growth_protocol_ch1 | Otic vesicles from wild-type and Dlx5-null embryos were microdissected from mouse developmental stages E10 and E10.5 in ice-cold PBS (calcium and magnesium free). These were timed-pregnancies determined by a vaginal plug, and each embryo was staged independently in a litter by the number of somites. Once the vesicles were isolated as cleanly as possible from the embryos, they were placed in 1mg/ml solution of dispase dissolved in PBS (calcium and magnesium free) for 10-15 minutes on ice to facilitate the removal of closely attached mesenchyme. For each stage and genotype two biological replicates were collected, each comprising between 4 and 8 otic vesicles. For the 2B1 cell line, two independent cultures were used for both the empty vector-transfected and the Dlx5- transfected samples. Cells were grown in chick embryo fibroblast medium at 32oC to a confluency of 70-80% in the presence of gamma-interferon, then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | To synthesize biotin-labeled target (cRNA) for hybridization to Affymetrix arrays, 22ul of the purified cDNA were used as template in in-vitro transcription reactions using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, NY). Besides the template cDNA, all other components were added following the instructions provided by the manufacturer, and reactions were incubated at 37oC for 10 hours on the PCR machine mentioned above under 'extract protocol'. Labeled cRNA was purified using an RNA purification kit (Qiagen) following the manufacturer’s instructions and eluted in 50ul of water.
| | Sample_hyb_protocol | Fragmentation of cRNA was carried out following the standard Affymetrix procedure, and 10ug of fragmented cRNA from each sample was hybridized to the Mouse Genome 430 2.0 gene chips for 16-18 hours at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000.
| | Sample_data_processing | Analysis was carried out in Expression Console software (Affymetrix) by employing the Robust Multichip Analysis (RMA) algorithm. All normalized (log-base-2) expression values below 5.5 were considered ‘Absent’. For cell line microarray data the cut-off for making ‘Present’ calls was set to 4.8 since this was the expression of Dlx5 in Dlx5-transfected cells.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Samin,,Sajan
| | Sample_contact_institute | University of Chicago
| | Sample_contact_address | 920 E. 58th Street, CLSC 317
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60637
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556783/suppl/GSM556783.CEL.gz
| | Sample_series_id | GSE22381
| | Sample_data_row_count | 45101
| | |
|
GSM556784 | GPL1261 |
|
E10.5_otic_vesicle_mut_replicate1
|
Mouse otic vesicle at E10.5 mut
|
tissue: inner ear
genotype/variation: Dlx5-null
age: E10.5
|
Otic vesicle at E10.5, replicate1
|
| Sample_geo_accession | GSM556784
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jun 16 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Otic vesicles were directly transferred into 1ml of TRIZOL. The 2B1 cell line was allowed to proliferate at 32oC in the presence of gamma-interferon to a confluency of 70-80% and then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_growth_protocol_ch1 | Otic vesicles from wild-type and Dlx5-null embryos were microdissected from mouse developmental stages E10 and E10.5 in ice-cold PBS (calcium and magnesium free). These were timed-pregnancies determined by a vaginal plug, and each embryo was staged independently in a litter by the number of somites. Once the vesicles were isolated as cleanly as possible from the embryos, they were placed in 1mg/ml solution of dispase dissolved in PBS (calcium and magnesium free) for 10-15 minutes on ice to facilitate the removal of closely attached mesenchyme. For each stage and genotype two biological replicates were collected, each comprising between 4 and 8 otic vesicles. For the 2B1 cell line, two independent cultures were used for both the empty vector-transfected and the Dlx5- transfected samples. Cells were grown in chick embryo fibroblast medium at 32oC to a confluency of 70-80% in the presence of gamma-interferon, then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | To synthesize biotin-labeled target (cRNA) for hybridization to Affymetrix arrays, 22ul of the purified cDNA were used as template in in-vitro transcription reactions using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, NY). Besides the template cDNA, all other components were added following the instructions provided by the manufacturer, and reactions were incubated at 37oC for 10 hours on the PCR machine mentioned above under 'extract protocol'. Labeled cRNA was purified using an RNA purification kit (Qiagen) following the manufacturer’s instructions and eluted in 50ul of water.
| | Sample_hyb_protocol | Fragmentation of cRNA was carried out following the standard Affymetrix procedure, and 10ug of fragmented cRNA from each sample was hybridized to the Mouse Genome 430 2.0 gene chips for 16-18 hours at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000.
| | Sample_data_processing | Analysis was carried out in Expression Console software (Affymetrix) by employing the Robust Multichip Analysis (RMA) algorithm. All normalized (log-base-2) expression values below 5.5 were considered ‘Absent’. For cell line microarray data the cut-off for making ‘Present’ calls was set to 4.8 since this was the expression of Dlx5 in Dlx5-transfected cells.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Samin,,Sajan
| | Sample_contact_institute | University of Chicago
| | Sample_contact_address | 920 E. 58th Street, CLSC 317
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60637
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556784/suppl/GSM556784.CEL.gz
| | Sample_series_id | GSE22381
| | Sample_data_row_count | 45101
| | |
|
GSM556785 | GPL1261 |
|
E10.5_otic_vesicle_mut_replicate2
|
Mouse otic vesicle at E10.5 mut
|
tissue: inner ear
genotype/variation: Dlx5-null
age: E10.5
|
Otic vesicle at E10.5, replicate1
|
| Sample_geo_accession | GSM556785
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jun 16 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Otic vesicles were directly transferred into 1ml of TRIZOL. The 2B1 cell line was allowed to proliferate at 32oC in the presence of gamma-interferon to a confluency of 70-80% and then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_growth_protocol_ch1 | Otic vesicles from wild-type and Dlx5-null embryos were microdissected from mouse developmental stages E10 and E10.5 in ice-cold PBS (calcium and magnesium free). These were timed-pregnancies determined by a vaginal plug, and each embryo was staged independently in a litter by the number of somites. Once the vesicles were isolated as cleanly as possible from the embryos, they were placed in 1mg/ml solution of dispase dissolved in PBS (calcium and magnesium free) for 10-15 minutes on ice to facilitate the removal of closely attached mesenchyme. For each stage and genotype two biological replicates were collected, each comprising between 4 and 8 otic vesicles. For the 2B1 cell line, two independent cultures were used for both the empty vector-transfected and the Dlx5- transfected samples. Cells were grown in chick embryo fibroblast medium at 32oC to a confluency of 70-80% in the presence of gamma-interferon, then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | To synthesize biotin-labeled target (cRNA) for hybridization to Affymetrix arrays, 22ul of the purified cDNA were used as template in in-vitro transcription reactions using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, NY). Besides the template cDNA, all other components were added following the instructions provided by the manufacturer, and reactions were incubated at 37oC for 10 hours on the PCR machine mentioned above under 'extract protocol'. Labeled cRNA was purified using an RNA purification kit (Qiagen) following the manufacturer’s instructions and eluted in 50ul of water.
| | Sample_hyb_protocol | Fragmentation of cRNA was carried out following the standard Affymetrix procedure, and 10ug of fragmented cRNA from each sample was hybridized to the Mouse Genome 430 2.0 gene chips for 16-18 hours at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000.
| | Sample_data_processing | Analysis was carried out in Expression Console software (Affymetrix) by employing the Robust Multichip Analysis (RMA) algorithm. All normalized (log-base-2) expression values below 5.5 were considered ‘Absent’. For cell line microarray data the cut-off for making ‘Present’ calls was set to 4.8 since this was the expression of Dlx5 in Dlx5-transfected cells.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Samin,,Sajan
| | Sample_contact_institute | University of Chicago
| | Sample_contact_address | 920 E. 58th Street, CLSC 317
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60637
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556785/suppl/GSM556785.CEL.gz
| | Sample_series_id | GSE22381
| | Sample_data_row_count | 45101
| | |
|
GSM556786 | GPL1261 |
|
2B1_Dlx5_replicate1
|
2B1 Otic vesicle cell line over-expressing Dlx5 and GFP
|
tissue: 2B1 cell line
genotype/variation: N/A
age: 4 days post-differentiation in-vitro
|
2B1 Otic vesicle cell line transiently transfected with Dlx5 and GFP expression vector and differentiated for 4 days at 37oC without gamma-interferon, replicate1
|
| Sample_geo_accession | GSM556786
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jun 16 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Otic vesicles were directly transferred into 1ml of TRIZOL. The 2B1 cell line was allowed to proliferate at 32oC in the presence of gamma-interferon to a confluency of 70-80% and then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_growth_protocol_ch1 | Otic vesicles from wild-type and Dlx5-null embryos were microdissected from mouse developmental stages E10 and E10.5 in ice-cold PBS (calcium and magnesium free). These were timed-pregnancies determined by a vaginal plug, and each embryo was staged independently in a litter by the number of somites. Once the vesicles were isolated as cleanly as possible from the embryos, they were placed in 1mg/ml solution of dispase dissolved in PBS (calcium and magnesium free) for 10-15 minutes on ice to facilitate the removal of closely attached mesenchyme. For each stage and genotype two biological replicates were collected, each comprising between 4 and 8 otic vesicles. For the 2B1 cell line, two independent cultures were used for both the empty vector-transfected and the Dlx5- transfected samples. Cells were grown in chick embryo fibroblast medium at 32oC to a confluency of 70-80% in the presence of gamma-interferon, then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | To synthesize biotin-labeled target (cRNA) for hybridization to Affymetrix arrays, 22ul of the purified cDNA were used as template in in-vitro transcription reactions using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, NY). Besides the template cDNA, all other components were added following the instructions provided by the manufacturer, and reactions were incubated at 37oC for 10 hours on the PCR machine mentioned above under 'extract protocol'. Labeled cRNA was purified using an RNA purification kit (Qiagen) following the manufacturer’s instructions and eluted in 50ul of water.
| | Sample_hyb_protocol | Fragmentation of cRNA was carried out following the standard Affymetrix procedure, and 10ug of fragmented cRNA from each sample was hybridized to the Mouse Genome 430 2.0 gene chips for 16-18 hours at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000.
| | Sample_data_processing | Analysis was carried out in Expression Console software (Affymetrix) by employing the Robust Multichip Analysis (RMA) algorithm. All normalized (log-base-2) expression values below 5.5 were considered ‘Absent’. For cell line microarray data the cut-off for making ‘Present’ calls was set to 4.8 since this was the expression of Dlx5 in Dlx5-transfected cells.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Samin,,Sajan
| | Sample_contact_institute | University of Chicago
| | Sample_contact_address | 920 E. 58th Street, CLSC 317
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60637
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556786/suppl/GSM556786.CEL.gz
| | Sample_series_id | GSE22381
| | Sample_data_row_count | 45101
| | |
|
GSM556787 | GPL1261 |
|
2B1_Dlx5_replicate2
|
2B1 Otic vesicle cell line over-expressing Dlx5 and GFP
|
tissue: 2B1 cell line
genotype/variation: N/A
age: 4 days post-differentiation in-vitro
|
2B1 Otic vesicle cell line transiently transfected with Dlx5 and GFP expression vector and differentiated for 4 days at 37oC without gamma-interferon, replicate2
|
| Sample_geo_accession | GSM556787
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jun 16 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Otic vesicles were directly transferred into 1ml of TRIZOL. The 2B1 cell line was allowed to proliferate at 32oC in the presence of gamma-interferon to a confluency of 70-80% and then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_growth_protocol_ch1 | Otic vesicles from wild-type and Dlx5-null embryos were microdissected from mouse developmental stages E10 and E10.5 in ice-cold PBS (calcium and magnesium free). These were timed-pregnancies determined by a vaginal plug, and each embryo was staged independently in a litter by the number of somites. Once the vesicles were isolated as cleanly as possible from the embryos, they were placed in 1mg/ml solution of dispase dissolved in PBS (calcium and magnesium free) for 10-15 minutes on ice to facilitate the removal of closely attached mesenchyme. For each stage and genotype two biological replicates were collected, each comprising between 4 and 8 otic vesicles. For the 2B1 cell line, two independent cultures were used for both the empty vector-transfected and the Dlx5- transfected samples. Cells were grown in chick embryo fibroblast medium at 32oC to a confluency of 70-80% in the presence of gamma-interferon, then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | To synthesize biotin-labeled target (cRNA) for hybridization to Affymetrix arrays, 22ul of the purified cDNA were used as template in in-vitro transcription reactions using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, NY). Besides the template cDNA, all other components were added following the instructions provided by the manufacturer, and reactions were incubated at 37oC for 10 hours on the PCR machine mentioned above under 'extract protocol'. Labeled cRNA was purified using an RNA purification kit (Qiagen) following the manufacturer’s instructions and eluted in 50ul of water.
| | Sample_hyb_protocol | Fragmentation of cRNA was carried out following the standard Affymetrix procedure, and 10ug of fragmented cRNA from each sample was hybridized to the Mouse Genome 430 2.0 gene chips for 16-18 hours at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000.
| | Sample_data_processing | Analysis was carried out in Expression Console software (Affymetrix) by employing the Robust Multichip Analysis (RMA) algorithm. All normalized (log-base-2) expression values below 5.5 were considered ‘Absent’. For cell line microarray data the cut-off for making ‘Present’ calls was set to 4.8 since this was the expression of Dlx5 in Dlx5-transfected cells.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Samin,,Sajan
| | Sample_contact_institute | University of Chicago
| | Sample_contact_address | 920 E. 58th Street, CLSC 317
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60637
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556787/suppl/GSM556787.CEL.gz
| | Sample_series_id | GSE22381
| | Sample_data_row_count | 45101
| | |
|
GSM556788 | GPL1261 |
|
2B1_empty_vector_replicate1
|
2B1 Otic vesicle cell line over-expressing GFP only
|
tissue: 2B1 cell line
genotype/variation: N/A
age: 4 days post-differentiation in-vitro
|
2B1 Otic vesicle cell line transiently transfected with an empty vector only containing GFP and differentiated for 4 days at 37oC without gamma-interferon, replicate1
|
| Sample_geo_accession | GSM556788
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jun 16 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Otic vesicles were directly transferred into 1ml of TRIZOL. The 2B1 cell line was allowed to proliferate at 32oC in the presence of gamma-interferon to a confluency of 70-80% and then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_growth_protocol_ch1 | Otic vesicles from wild-type and Dlx5-null embryos were microdissected from mouse developmental stages E10 and E10.5 in ice-cold PBS (calcium and magnesium free). These were timed-pregnancies determined by a vaginal plug, and each embryo was staged independently in a litter by the number of somites. Once the vesicles were isolated as cleanly as possible from the embryos, they were placed in 1mg/ml solution of dispase dissolved in PBS (calcium and magnesium free) for 10-15 minutes on ice to facilitate the removal of closely attached mesenchyme. For each stage and genotype two biological replicates were collected, each comprising between 4 and 8 otic vesicles. For the 2B1 cell line, two independent cultures were used for both the empty vector-transfected and the Dlx5- transfected samples. Cells were grown in chick embryo fibroblast medium at 32oC to a confluency of 70-80% in the presence of gamma-interferon, then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | To synthesize biotin-labeled target (cRNA) for hybridization to Affymetrix arrays, 22ul of the purified cDNA were used as template in in-vitro transcription reactions using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, NY). Besides the template cDNA, all other components were added following the instructions provided by the manufacturer, and reactions were incubated at 37oC for 10 hours on the PCR machine mentioned above under 'extract protocol'. Labeled cRNA was purified using an RNA purification kit (Qiagen) following the manufacturer’s instructions and eluted in 50ul of water.
| | Sample_hyb_protocol | Fragmentation of cRNA was carried out following the standard Affymetrix procedure, and 10ug of fragmented cRNA from each sample was hybridized to the Mouse Genome 430 2.0 gene chips for 16-18 hours at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000.
| | Sample_data_processing | Analysis was carried out in Expression Console software (Affymetrix) by employing the Robust Multichip Analysis (RMA) algorithm. All normalized (log-base-2) expression values below 5.5 were considered ‘Absent’. For cell line microarray data the cut-off for making ‘Present’ calls was set to 4.8 since this was the expression of Dlx5 in Dlx5-transfected cells.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Samin,,Sajan
| | Sample_contact_institute | University of Chicago
| | Sample_contact_address | 920 E. 58th Street, CLSC 317
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60637
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556788/suppl/GSM556788.CEL.gz
| | Sample_series_id | GSE22381
| | Sample_data_row_count | 45101
| | |
|
GSM556789 | GPL1261 |
|
2B1_empty_vector_replicate2
|
2B1 Otic vesicle cell line over-expressing GFP only
|
tissue: 2B1 cell line
genotype/variation: N/A
age: 4 days post-differentiation in-vitro
|
2B1 Otic vesicle cell line transiently transfected with an empty vector only containing GFP and differentiated for 4 days at 37oC without gamma-interferon, replicate2
|
| Sample_geo_accession | GSM556789
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jun 16 2010
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Otic vesicles were directly transferred into 1ml of TRIZOL. The 2B1 cell line was allowed to proliferate at 32oC in the presence of gamma-interferon to a confluency of 70-80% and then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_growth_protocol_ch1 | Otic vesicles from wild-type and Dlx5-null embryos were microdissected from mouse developmental stages E10 and E10.5 in ice-cold PBS (calcium and magnesium free). These were timed-pregnancies determined by a vaginal plug, and each embryo was staged independently in a litter by the number of somites. Once the vesicles were isolated as cleanly as possible from the embryos, they were placed in 1mg/ml solution of dispase dissolved in PBS (calcium and magnesium free) for 10-15 minutes on ice to facilitate the removal of closely attached mesenchyme. For each stage and genotype two biological replicates were collected, each comprising between 4 and 8 otic vesicles. For the 2B1 cell line, two independent cultures were used for both the empty vector-transfected and the Dlx5- transfected samples. Cells were grown in chick embryo fibroblast medium at 32oC to a confluency of 70-80% in the presence of gamma-interferon, then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | To synthesize biotin-labeled target (cRNA) for hybridization to Affymetrix arrays, 22ul of the purified cDNA were used as template in in-vitro transcription reactions using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, NY). Besides the template cDNA, all other components were added following the instructions provided by the manufacturer, and reactions were incubated at 37oC for 10 hours on the PCR machine mentioned above under 'extract protocol'. Labeled cRNA was purified using an RNA purification kit (Qiagen) following the manufacturer’s instructions and eluted in 50ul of water.
| | Sample_hyb_protocol | Fragmentation of cRNA was carried out following the standard Affymetrix procedure, and 10ug of fragmented cRNA from each sample was hybridized to the Mouse Genome 430 2.0 gene chips for 16-18 hours at 45oC.
| | Sample_scan_protocol | GeneChips were scanned using GeneChip Scanner 3000.
| | Sample_data_processing | Analysis was carried out in Expression Console software (Affymetrix) by employing the Robust Multichip Analysis (RMA) algorithm. All normalized (log-base-2) expression values below 5.5 were considered ‘Absent’. For cell line microarray data the cut-off for making ‘Present’ calls was set to 4.8 since this was the expression of Dlx5 in Dlx5-transfected cells.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Samin,,Sajan
| | Sample_contact_institute | University of Chicago
| | Sample_contact_address | 920 E. 58th Street, CLSC 317
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60637
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM556nnn/GSM556789/suppl/GSM556789.CEL.gz
| | Sample_series_id | GSE22381
| | Sample_data_row_count | 45101
| | |
|
| |
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