Search results for the GEO ID: GSE49522  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1200410 | GPL339 |
|
CBA Inferior colliculus Mice-4
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Young Control
|
|
| Sample_geo_accession | GSM1200410
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200410/suppl/GSM1200410_4_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200410/suppl/GSM1200410_4_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200411 | GPL339 |
|
CBA Inferior colliculus Mice-5
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Young Control
|
|
| Sample_geo_accession | GSM1200411
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200411/suppl/GSM1200411_5_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200411/suppl/GSM1200411_5_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200412 | GPL339 |
|
CBA Inferior colliculus Mice-6
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Young Control
|
|
| Sample_geo_accession | GSM1200412
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200412/suppl/GSM1200412_6_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200412/suppl/GSM1200412_6_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200413 | GPL339 |
|
CBA Inferior colliculus Mice-17
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Young Control
|
|
| Sample_geo_accession | GSM1200413
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200413/suppl/GSM1200413_17_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200413/suppl/GSM1200413_17_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200414 | GPL339 |
|
CBA Inferior colliculus Mice-18
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Young Control
|
|
| Sample_geo_accession | GSM1200414
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200414/suppl/GSM1200414_18_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200414/suppl/GSM1200414_18_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200415 | GPL339 |
|
CBA Inferior colliculus Mice-25
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Young Control
|
|
| Sample_geo_accession | GSM1200415
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200415/suppl/GSM1200415_25_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200415/suppl/GSM1200415_25_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200416 | GPL339 |
|
CBA Inferior colliculus Mice-36
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Young Control
|
|
| Sample_geo_accession | GSM1200416
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200416/suppl/GSM1200416_36_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200416/suppl/GSM1200416_36_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200417 | GPL339 |
|
CBA Inferior colliculus Mice-41
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Young Control
|
|
| Sample_geo_accession | GSM1200417
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200417/suppl/GSM1200417_41_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200417/suppl/GSM1200417_41_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200418 | GPL339 |
|
CBA Inferior colliculus Mice-7
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200418
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200418/suppl/GSM1200418_7_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200418/suppl/GSM1200418_7_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200419 | GPL339 |
|
CBA Inferior colliculus Mice-8
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200419
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200419/suppl/GSM1200419_8_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200419/suppl/GSM1200419_8_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200420 | GPL339 |
|
CBA Inferior colliculus Mice-9
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200420
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200420/suppl/GSM1200420_9_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200420/suppl/GSM1200420_9_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200421 | GPL339 |
|
CBA Inferior colliculus Mice-10
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200421
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200421/suppl/GSM1200421_10_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200421/suppl/GSM1200421_10_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200422 | GPL339 |
|
CBA Inferior colliculus Mice-14
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200422
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200422/suppl/GSM1200422_14_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200422/suppl/GSM1200422_14_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200423 | GPL339 |
|
CBA Inferior colliculus Mice-15
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200423
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200423/suppl/GSM1200423_15_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200423/suppl/GSM1200423_15_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200424 | GPL339 |
|
CBA Inferior colliculus Mice-19
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200424
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200424/suppl/GSM1200424_19_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200424/suppl/GSM1200424_19_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200425 | GPL339 |
|
CBA Inferior colliculus Mice-20
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200425
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200425/suppl/GSM1200425_20_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200425/suppl/GSM1200425_20_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200426 | GPL339 |
|
CBA Inferior colliculus Mice-23
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200426
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200426/suppl/GSM1200426_23_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200426/suppl/GSM1200426_23_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200427 | GPL339 |
|
CBA Inferior colliculus Mice-24
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200427
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200427/suppl/GSM1200427_24_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200427/suppl/GSM1200427_24_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200428 | GPL339 |
|
CBA Inferior colliculus Mice-26
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200428
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200428/suppl/GSM1200428_26_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200428/suppl/GSM1200428_26_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200429 | GPL339 |
|
CBA Inferior colliculus Mice-27
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200429
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200429/suppl/GSM1200429_27_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200429/suppl/GSM1200429_27_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200430 | GPL339 |
|
CBA Inferior colliculus Mice-28
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200430
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200430/suppl/GSM1200430_28_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200430/suppl/GSM1200430_28_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200431 | GPL339 |
|
CBA Inferior colliculus Mice-29
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200431
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200431/suppl/GSM1200431_29_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200431/suppl/GSM1200431_29_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200432 | GPL339 |
|
CBA Inferior colliculus Mice-31
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200432
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200432/suppl/GSM1200432_31_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200432/suppl/GSM1200432_31_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200433 | GPL339 |
|
CBA Inferior colliculus Mice-38
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200433
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200433/suppl/GSM1200433_38_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200433/suppl/GSM1200433_38_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200434 | GPL339 |
|
CBA Inferior colliculus Mice-39
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Middle-Aged
|
|
| Sample_geo_accession | GSM1200434
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200434/suppl/GSM1200434_39_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200434/suppl/GSM1200434_39_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200435 | GPL339 |
|
CBA Inferior colliculus Mice-2
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Mild Presbycusis
|
|
| Sample_geo_accession | GSM1200435
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200435/suppl/GSM1200435_2_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200435/suppl/GSM1200435_2_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200436 | GPL339 |
|
CBA Inferior colliculus Mice-3
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Mild Presbycusis
|
|
| Sample_geo_accession | GSM1200436
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200436/suppl/GSM1200436_3_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200436/suppl/GSM1200436_3_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200437 | GPL339 |
|
CBA Inferior colliculus Mice-12
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Mild Presbycusis
|
|
| Sample_geo_accession | GSM1200437
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200437/suppl/GSM1200437_12_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200437/suppl/GSM1200437_12_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200438 | GPL339 |
|
CBA Inferior colliculus Mice-21
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Mild Presbycusis
|
|
| Sample_geo_accession | GSM1200438
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200438/suppl/GSM1200438_21_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200438/suppl/GSM1200438_21_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200439 | GPL339 |
|
CBA Inferior colliculus Mice-22
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Mild Presbycusis
|
|
| Sample_geo_accession | GSM1200439
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200439/suppl/GSM1200439_22_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200439/suppl/GSM1200439_22_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200440 | GPL339 |
|
CBA Inferior colliculus Mice-37
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Mild Presbycusis
|
|
| Sample_geo_accession | GSM1200440
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200440/suppl/GSM1200440_37_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200440/suppl/GSM1200440_37_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200441 | GPL339 |
|
CBA Inferior colliculus Mice-34
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Mild Presbycusis
|
|
| Sample_geo_accession | GSM1200441
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200441/suppl/GSM1200441_34_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200441/suppl/GSM1200441_34_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200442 | GPL339 |
|
CBA Inferior colliculus Mice-35
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Mild Presbycusis
|
|
| Sample_geo_accession | GSM1200442
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200442/suppl/GSM1200442_35_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200442/suppl/GSM1200442_35_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200443 | GPL339 |
|
CBA Inferior colliculus Mice-40
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Mild Presbycusis
|
|
| Sample_geo_accession | GSM1200443
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200443/suppl/GSM1200443_40_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200443/suppl/GSM1200443_40_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200444 | GPL339 |
|
CBA Inferior colliculus Mice-1
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Severe Presbycusis
|
|
| Sample_geo_accession | GSM1200444
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200444/suppl/GSM1200444_1_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200444/suppl/GSM1200444_1_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200445 | GPL339 |
|
CBA Inferior colliculus Mice-11
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Severe Presbycusis
|
|
| Sample_geo_accession | GSM1200445
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200445/suppl/GSM1200445_11_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200445/suppl/GSM1200445_11_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200446 | GPL339 |
|
CBA Inferior colliculus Mice-30
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Severe Presbycusis
|
|
| Sample_geo_accession | GSM1200446
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200446/suppl/GSM1200446_30_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200446/suppl/GSM1200446_30_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200447 | GPL339 |
|
CBA Inferior colliculus Mice-32
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Male
hearing status: Severe Presbycusis
|
|
| Sample_geo_accession | GSM1200447
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200447/suppl/GSM1200447_32_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200447/suppl/GSM1200447_32_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
|
GSM1200448 | GPL339 |
|
CBA Inferior colliculus Mice-33
|
CBA mice Inferior colliculus
|
strain: CBA/CaJ
gender: Female
hearing status: Severe Presbycusis
|
|
| Sample_geo_accession | GSM1200448
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Aug 02 2013
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | No treatment, normal aging mice
| | Sample_growth_protocol_ch1 | CBA/CaJ mice were in-bred in house according to university of rochester vivarium and animal use committee protocols. Original breeding pairs were obtained from Jackson Laboratories. All animals had similar environmental and non-ototoxic histories, being raised together in a relatively quiet vivarium room.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Several days later, upon completion of the physiological, recording sessions, the mice were sacrificed by decapitation.The inferior colliculus from the midbrains were immediately dissected using a Zeiss stereomicroscope and placed in ice-cold saline. The IC was dissected from each brain. Forty pairs of cochleae and 39 brain (IC) samples were collected. The soft tissue of the cochlear duct from the two cochleae of each animal were combined as one gene expression sample. All samples were placed in cold Trizol (Invitrogen, CA)and stored at −80 ◦C for gene microarray and real-time PCR processing.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Clean up of double-stranded cDNA was done according to the Affymetrix GeneChip Expression analysis protocol. Synthesis of Biotin-labeled cRNAwas performed by adding 1 g of cDNA to 10×IVT labeling buffer, IVT labeling NTP mix, IVT labeling enzyme mix, and RNase-free water, then incubated at 37 ◦Cfor 16 h. The Biotin-labeledcRNAwas cleaned up according to the Affymertix GeneChip expression analysis protocol and a 20 g of full-length cRNA from each sample was fragmented by adding 5× fragmentation buffer and RNase-freewater, followed by incubation at 94 ◦Cfor 35 min. The standard fragmentation procedure produces a distribution of RNA fragment sizes from approximately 35–200 bases. After the fragmentation, cDNA, full-length cRNA and fragmented cRNA were analyzed by electrophoresis using the Agilent Bioanalyzer 2100 to assess the appropriate size distribution prior to microarray hybridization.
| | Sample_hyb_protocol | GeneChip M430A probe arrays (Affymetrix) were hybridized, washed, and stained according to the manufacturer’s instructions in a fluidics station.
| | Sample_scan_protocol | The arrays were scanned using a Hewlett Packard confocal laser scanner and visualized using GeneChip 5.1 software. Three data files were created, namely image data (.dat), cell intensity data (.cel), and expression probe analysis data (.chp) files.
| | Sample_data_processing | The software used for normalization was GeneTraffic 3.1, for more information available at Iobion,http://www.iobion.com.
| | Sample_platform_id | GPL339
| | Sample_contact_name | Robert,,Frisina
| | Sample_contact_email | rfrisina@usf.edu
| | Sample_contact_phone | 813-974-4013
| | Sample_contact_laboratory | Global center for hearing &Speech Research
| | Sample_contact_department | Department of Chemical & Biomedical Engineering
| | Sample_contact_institute | university of south florida
| | Sample_contact_address | 4202. E. Fowler Avenue ENB 118
| | Sample_contact_city | Tampa
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 33620
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200448/suppl/GSM1200448_33_Frisina_S2_M430A.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1200nnn/GSM1200448/suppl/GSM1200448_33_Frisina_S2_M430A.CHP.gz
| | Sample_series_id | GSE49522
| | Sample_data_row_count | 22690
| | |
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