Search results for the GEO ID: GSE12810  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM321743 | GPL1261 |
|
Modioli_noise-exposed_rep1
|
Left and right cochlear modiolus, previously noise-exposed, animal 'DA'
|
aliases: '149', 'DA'
biological replicate: 1 of 3
strain: CBA/CaJ
gender: female
date of birth: 7/21/2004
litter number: 7
individual number: 1
date of noise exposure: 8/18/2004
date of sacrifice: 9/16/2004
tissue: left and right modioli dissected from cochlea
total rna: 15 ng
amplified cdna: 5.4 micrograms
fragmented and biotinylated cdna: 4.0 micrograms
|
n/a
|
| Sample_geo_accession | GSM321743
| | Sample_status | Public on Sep 16 2009
| | Sample_submission_date | Sep 17 2008
| | Sample_last_update_date | Feb 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Laboratories of Drs. Albert S. Feng and Richard Kollmar
| | Sample_treatment_protocol_ch1 | At four weeks of age, 'treated' animals were exposed together for five hours to two-octave band-limited noise (5-20 kHz) at 110 dB SPL. The animals were distributed between two empty 10-gallon glass tanks inside an acoustic isolation chamber in a separate room. A model S81-02 noise generator (Coulbourn, Whitehall, PA), a model GFP-555II preamplifier (Adcom, Scottsdale, AZ), and a model XL-600 power amplifier (Hafler, Tempe, AZ) drove one model 100HT high-efficiency horn tweeter with a flat frequency response from 2 to 20 kHz (Fostex, Boonton, NJ) over each tank. The noise level was monitored with a model 2239 sound level meter (Brüel & Kjær, Nærum, Denmark). The animals' behavior did not change during the noise exposure. 'Untreated' (negative-control) animals remained in the holding room throughout the experiment and were not exposed to elevated noise levels.
| | Sample_growth_protocol_ch1 | Noise-exposed and negative-control animals were kept next to each other in the same holding room of the animal facility at the Beckman Institute and maintained according to standard procedures. All experiments were conducted in accordance with protocols approved by the University of Illinois Institutional Animal Care and Use Committee.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Both treated and untreated animals were sacrificed at 8 weeks of age. Modioli were rapidly dissected in physiological saline (within 8 min after sacrifice), dissolved in Trizol (Invitrogen, Carlsbad, CA) with a small rotor-stator homogenizer (Tissue-Tearor; Biospec Products, Bartlesville, OK), and stored at -80°C. Total RNA was extracted from all samples in parallel, with glycogen added to maximize precipitation. The resuspended RNA was further purified by adsorption to silica-gel-membrane spin columns (RNeasy MinElute Cleanup kit; Qiagen, Valencia, CA) and eluted in a minimal volume of water. The concentration of the RNA was determined by fluorometry (RiboGreen; Invitrogen), and its integrity was confirmed by electrophoresis (2100 Bioanalyzer; Agilent, Santa Clara, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The entire RNA sample was reverse transcribed, linearly amplified, fragmented, and biotinylated with an Ovation Biotin kit version 1.0 (NuGEN, San Carlos, CA). The cDNA concentrations after amplification and labeling were determined by spectrophotometry.
| | Sample_hyb_protocol | The biotinylated cDNA was hybridized to a Mouse Expression Set 430 2.0 array in a Hybridization Oven 640 (Affymetrix, Santa Clara, CA). After 16 hours, the array was stained and washed in a Fluidics Station 450 (Affymetrix) according to protocol EukGE-WS2v4_450.
| | Sample_scan_protocol | The stained array was imaged in a Gene Chip Scanner 3000 (Affymetrix)
| | Sample_scan_protocol | at a resolution of 1.56 µm per pixel and a wavelength of 570 nm. The probe hybridization signals (cell intensity data) were extracted from the .DAT image file with Affymetrix software and saved as a .CEL file. Both hybridization and scan steps were performed at the Roy J. Carver Biotechnology Center of the University of Illinois at Urbana-Champaign.
| | Sample_data_processing | The probe hybridization signals of all six samples (files 149_E.CEL to 154_E.CEL) were pre-processed together with Bioconductor tools (release 2.1; www.bioconductor.org) in R software (version 2.6.1; http://www.r-project.org) according to the procedures outlined in Gentleman et al. (2005) by using the following commands:
| | Sample_data_processing | #################
| | Sample_data_processing | ### Importing ###
| | Sample_data_processing | # import .CEL files in working directory into Affybatch object RK111904_CELs
| | Sample_data_processing | > library("affy")
| | Sample_data_processing | > RK111904_CELs <- ReadAffy()
| | Sample_data_processing | #######################
| | Sample_data_processing | ### Quality Control ###
| | Sample_data_processing | # Simple and Affymetrix-style quality control of hybridization data
| | Sample_data_processing | > library(affyQCReport)
| | Sample_data_processing | > QCReport(RK111904_CELs,file="affyQCReport.pdf")
| | Sample_data_processing | # Check for RNA degradation
| | Sample_data_processing | > RNAdeg <- AffyRNAdeg(RK111904_CELs)
| | Sample_data_processing = > plotAffyRNAdeg(RNAdeg, col | c(2,3,2,3,3,2))
| | Sample_data_processing | > summaryAffyRNAdeg(RNAdeg)
| | Sample_data_processing | # Check for abnormal population distributions of hybridization signals
| | Sample_data_processing | > library(geneplotter)
| | Sample_data_processing = > MAplot(RK111904_CELs,pairs=TRUE,plot.method="smoothScatter", cex | 1.2)
| | Sample_data_processing | # Check for abnormal spatial distributions of hybridization signals
| | Sample_data_processing | > library(affyPLM)
| | Sample_data_processing = > options(width | 40)
| | Sample_data_processing | > Pset <- fitPLM(RK111904_CELs)
| | Sample_data_processing = > image(Pset, which = 1, type | "sign.resids")
| | Sample_data_processing | > ...
| | Sample_data_processing = > RLE(Pset, main = "RLE for RK111904_CELs", ylim | c(-6,7))
| | Sample_data_processing = > NUSE(Pset, main = "NUSE for RK111904_CELs", ylim | c(0.85,1.5))
| | Sample_data_processing | ######################
| | Sample_data_processing | ### Pre-processing ###
| | Sample_data_processing | # Background correction, normalization, PM correction, and summarization
| | Sample_data_processing | > RK111904_fullEset <- expresso(RK111904_CELs,bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish")
| | Sample_data_processing | The quality-control step did not uncover notable defects other than a higher background level in file 154_E.CEL, which was corrected in the pre-processing step. For each sample, the paired Affymetrix probe-set IDs (ID_REF) and pre-processed expression levels (VALUE) were then exported as text files.
| | Sample_data_processing | Reference: Gentleman R., Huber W., Carey V.J., Irizarry R., Smith C., Zhang J., Li X., Scholtens D., Ding B., and Dudoit S. (eds). Bioinformatics and Computational Biology Solutions Using R and Bioconductor. London: Springer. 2005.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Richard,,Kollmar
| | Sample_contact_institute | University of Illinois at Urbana-Champaign
| | Sample_contact_address | 407 S. Goodwin Ave., MC-114
| | Sample_contact_city | Urbana
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 61801
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM321nnn/GSM321743/suppl/GSM321743.CEL.gz
| | Sample_series_id | GSE12810
| | Sample_data_row_count | 45101
| | |
|
GSM321744 | GPL1261 |
|
Modioli_noise-exposed_rep2
|
Left and right cochlear modiolus, previously noise-exposed, animal 'DB'
|
aliases: '150', 'DB'
biological replicate: 2 of 3
strain: CBA/CaJ
gender: female
date of birth: 7/21/2004
litter number: 7
individual number: 2
date of noise exposure: 8/18/2004
date of sacrifice: 9/16/2004
tissue: left and right modioli dissected from cochlea
total rna: 18 ng
amplified cdna: 5.7 micrograms
fragmented and biotinylated cdna: 4.2 micrograms
|
n/a
|
| Sample_geo_accession | GSM321744
| | Sample_status | Public on Sep 16 2009
| | Sample_submission_date | Sep 17 2008
| | Sample_last_update_date | Feb 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Laboratories of Drs. Albert S. Feng and Richard Kollmar
| | Sample_treatment_protocol_ch1 | At four weeks of age, 'treated' animals were exposed together for five hours to two-octave band-limited noise (5-20 kHz) at 110 dB SPL. The animals were distributed between two empty 10-gallon glass tanks inside an acoustic isolation chamber in a separate room. A model S81-02 noise generator (Coulbourn, Whitehall, PA), a model GFP-555II preamplifier (Adcom, Scottsdale, AZ), and a model XL-600 power amplifier (Hafler, Tempe, AZ) drove one model 100HT high-efficiency horn tweeter with a flat frequency response from 2 to 20 kHz (Fostex, Boonton, NJ) over each tank. The noise level was monitored with a model 2239 sound level meter (Brüel & Kjær, Nærum, Denmark). The animals' behavior did not change during the noise exposure. 'Untreated' (negative-control) animals remained in the holding room throughout the experiment and were not exposed to elevated noise levels.
| | Sample_growth_protocol_ch1 | Noise-exposed and negative-control animals were kept next to each other in the same holding room of the animal facility at the Beckman Institute and maintained according to standard procedures. All experiments were conducted in accordance with protocols approved by the University of Illinois Institutional Animal Care and Use Committee.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Both treated and untreated animals were sacrificed at 8 weeks of age. Modioli were rapidly dissected in physiological saline (within 8 min after sacrifice), dissolved in Trizol (Invitrogen, Carlsbad, CA) with a small rotor-stator homogenizer (Tissue-Tearor; Biospec Products, Bartlesville, OK), and stored at -80°C. Total RNA was extracted from all samples in parallel, with glycogen added to maximize precipitation. The resuspended RNA was further purified by adsorption to silica-gel-membrane spin columns (RNeasy MinElute Cleanup kit; Qiagen, Valencia, CA) and eluted in a minimal volume of water. The concentration of the RNA was determined by fluorometry (RiboGreen; Invitrogen), and its integrity was confirmed by electrophoresis (2100 Bioanalyzer; Agilent, Santa Clara, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The entire RNA sample was reverse transcribed, linearly amplified, fragmented, and biotinylated with an Ovation Biotin kit version 1.0 (NuGEN, San Carlos, CA). The cDNA concentrations after amplification and labeling were determined by spectrophotometry.
| | Sample_hyb_protocol | The biotinylated cDNA was hybridized to a Mouse Expression Set 430 2.0 array in a Hybridization Oven 640 (Affymetrix, Santa Clara, CA). After 16 hours, the array was stained and washed in a Fluidics Station 450 (Affymetrix) according to protocol EukGE-WS2v4_450.
| | Sample_scan_protocol | The stained array was imaged in a Gene Chip Scanner 3000 (Affymetrix)
| | Sample_scan_protocol | at a resolution of 1.56 µm per pixel and a wavelength of 570 nm. The probe hybridization signals (cell intensity data) were extracted from the .DAT image file with Affymetrix software and saved as a .CEL file. Both hybridization and scan steps were performed at the Roy J. Carver Biotechnology Center of the University of Illinois at Urbana-Champaign.
| | Sample_data_processing | The probe hybridization signals of all six samples (files 149_E.CEL to 154_E.CEL) were pre-processed together with Bioconductor tools (release 2.1; www.bioconductor.org) in R software (version 2.6.1; http://www.r-project.org) according to the procedures outlined in Gentleman et al. (2005) by using the following commands:
| | Sample_data_processing | #################
| | Sample_data_processing | ### Importing ###
| | Sample_data_processing | # import .CEL files in working directory into Affybatch object RK111904_CELs
| | Sample_data_processing | > library("affy")
| | Sample_data_processing | > RK111904_CELs <- ReadAffy()
| | Sample_data_processing | #######################
| | Sample_data_processing | ### Quality Control ###
| | Sample_data_processing | # Simple and Affymetrix-style quality control of hybridization data
| | Sample_data_processing | > library(affyQCReport)
| | Sample_data_processing | > QCReport(RK111904_CELs,file="affyQCReport.pdf")
| | Sample_data_processing | # Check for RNA degradation
| | Sample_data_processing | > RNAdeg <- AffyRNAdeg(RK111904_CELs)
| | Sample_data_processing = > plotAffyRNAdeg(RNAdeg, col | c(2,3,2,3,3,2))
| | Sample_data_processing | > summaryAffyRNAdeg(RNAdeg)
| | Sample_data_processing | # Check for abnormal population distributions of hybridization signals
| | Sample_data_processing | > library(geneplotter)
| | Sample_data_processing = > MAplot(RK111904_CELs,pairs=TRUE,plot.method="smoothScatter", cex | 1.2)
| | Sample_data_processing | # Check for abnormal spatial distributions of hybridization signals
| | Sample_data_processing | > library(affyPLM)
| | Sample_data_processing = > options(width | 40)
| | Sample_data_processing | > Pset <- fitPLM(RK111904_CELs)
| | Sample_data_processing = > image(Pset, which = 1, type | "sign.resids")
| | Sample_data_processing | > ...
| | Sample_data_processing = > RLE(Pset, main = "RLE for RK111904_CELs", ylim | c(-6,7))
| | Sample_data_processing = > NUSE(Pset, main = "NUSE for RK111904_CELs", ylim | c(0.85,1.5))
| | Sample_data_processing | ######################
| | Sample_data_processing | ### Pre-processing ###
| | Sample_data_processing | # Background correction, normalization, PM correction, and summarization
| | Sample_data_processing | > RK111904_fullEset <- expresso(RK111904_CELs,bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish")
| | Sample_data_processing | The quality-control step did not uncover notable defects other than a higher background level in file 154_E.CEL, which was corrected in the pre-processing step. For each sample, the paired Affymetrix probe-set IDs (ID_REF) and pre-processed expression levels (VALUE) were then exported as text files.
| | Sample_data_processing | Reference: Gentleman R., Huber W., Carey V.J., Irizarry R., Smith C., Zhang J., Li X., Scholtens D., Ding B., and Dudoit S. (eds). Bioinformatics and Computational Biology Solutions Using R and Bioconductor. London: Springer. 2005.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Richard,,Kollmar
| | Sample_contact_institute | University of Illinois at Urbana-Champaign
| | Sample_contact_address | 407 S. Goodwin Ave., MC-114
| | Sample_contact_city | Urbana
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 61801
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM321nnn/GSM321744/suppl/GSM321744.CEL.gz
| | Sample_series_id | GSE12810
| | Sample_data_row_count | 45101
| | |
|
GSM321745 | GPL1261 |
|
Modioli_noise-exposed_rep3
|
Left and right cochlear modiolus, previously noise-exposed, animal 'DD'
|
aliases: '151', 'DD'
biological replicate: 3 of 3
strain: CBA/CaJ
gender: female
date of birth: 7/21/2004
litter number: 7
individual number: 4
date of noise exposure: 8/18/2004
date of sacrifice: 9/16/2004
tissue: left and right modioli dissected from cochlea
total rna: 10 ng
amplified cdna: 5.5 micrograms
fragmented and biotinylated cdna: 4.1 micrograms
|
n/a
|
| Sample_geo_accession | GSM321745
| | Sample_status | Public on Sep 16 2009
| | Sample_submission_date | Sep 17 2008
| | Sample_last_update_date | Feb 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Laboratories of Drs. Albert S. Feng and Richard Kollmar
| | Sample_treatment_protocol_ch1 | At four weeks of age, 'treated' animals were exposed together for five hours to two-octave band-limited noise (5-20 kHz) at 110 dB SPL. The animals were distributed between two empty 10-gallon glass tanks inside an acoustic isolation chamber in a separate room. A model S81-02 noise generator (Coulbourn, Whitehall, PA), a model GFP-555II preamplifier (Adcom, Scottsdale, AZ), and a model XL-600 power amplifier (Hafler, Tempe, AZ) drove one model 100HT high-efficiency horn tweeter with a flat frequency response from 2 to 20 kHz (Fostex, Boonton, NJ) over each tank. The noise level was monitored with a model 2239 sound level meter (Brüel & Kjær, Nærum, Denmark). The animals' behavior did not change during the noise exposure. 'Untreated' (negative-control) animals remained in the holding room throughout the experiment and were not exposed to elevated noise levels.
| | Sample_growth_protocol_ch1 | Noise-exposed and negative-control animals were kept next to each other in the same holding room of the animal facility at the Beckman Institute and maintained according to standard procedures. All experiments were conducted in accordance with protocols approved by the University of Illinois Institutional Animal Care and Use Committee.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Both treated and untreated animals were sacrificed at 8 weeks of age. Modioli were rapidly dissected in physiological saline (within 8 min after sacrifice), dissolved in Trizol (Invitrogen, Carlsbad, CA) with a small rotor-stator homogenizer (Tissue-Tearor; Biospec Products, Bartlesville, OK), and stored at -80°C. Total RNA was extracted from all samples in parallel, with glycogen added to maximize precipitation. The resuspended RNA was further purified by adsorption to silica-gel-membrane spin columns (RNeasy MinElute Cleanup kit; Qiagen, Valencia, CA) and eluted in a minimal volume of water. The concentration of the RNA was determined by fluorometry (RiboGreen; Invitrogen), and its integrity was confirmed by electrophoresis (2100 Bioanalyzer; Agilent, Santa Clara, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The entire RNA sample was reverse transcribed, linearly amplified, fragmented, and biotinylated with an Ovation Biotin kit version 1.0 (NuGEN, San Carlos, CA). The cDNA concentrations after amplification and labeling were determined by spectrophotometry.
| | Sample_hyb_protocol | The biotinylated cDNA was hybridized to a Mouse Expression Set 430 2.0 array in a Hybridization Oven 640 (Affymetrix, Santa Clara, CA). After 16 hours, the array was stained and washed in a Fluidics Station 450 (Affymetrix) according to protocol EukGE-WS2v4_450.
| | Sample_scan_protocol | The stained array was imaged in a Gene Chip Scanner 3000 (Affymetrix)
| | Sample_scan_protocol | at a resolution of 1.56 µm per pixel and a wavelength of 570 nm. The probe hybridization signals (cell intensity data) were extracted from the .DAT image file with Affymetrix software and saved as a .CEL file. Both hybridization and scan steps were performed at the Roy J. Carver Biotechnology Center of the University of Illinois at Urbana-Champaign.
| | Sample_data_processing | The probe hybridization signals of all six samples (files 149_E.CEL to 154_E.CEL) were pre-processed together with Bioconductor tools (release 2.1; www.bioconductor.org) in R software (version 2.6.1; http://www.r-project.org) according to the procedures outlined in Gentleman et al. (2005) by using the following commands:
| | Sample_data_processing | #################
| | Sample_data_processing | ### Importing ###
| | Sample_data_processing | # import .CEL files in working directory into Affybatch object RK111904_CELs
| | Sample_data_processing | > library("affy")
| | Sample_data_processing | > RK111904_CELs <- ReadAffy()
| | Sample_data_processing | #######################
| | Sample_data_processing | ### Quality Control ###
| | Sample_data_processing | # Simple and Affymetrix-style quality control of hybridization data
| | Sample_data_processing | > library(affyQCReport)
| | Sample_data_processing | > QCReport(RK111904_CELs,file="affyQCReport.pdf")
| | Sample_data_processing | # Check for RNA degradation
| | Sample_data_processing | > RNAdeg <- AffyRNAdeg(RK111904_CELs)
| | Sample_data_processing = > plotAffyRNAdeg(RNAdeg, col | c(2,3,2,3,3,2))
| | Sample_data_processing | > summaryAffyRNAdeg(RNAdeg)
| | Sample_data_processing | # Check for abnormal population distributions of hybridization signals
| | Sample_data_processing | > library(geneplotter)
| | Sample_data_processing = > MAplot(RK111904_CELs,pairs=TRUE,plot.method="smoothScatter", cex | 1.2)
| | Sample_data_processing | # Check for abnormal spatial distributions of hybridization signals
| | Sample_data_processing | > library(affyPLM)
| | Sample_data_processing = > options(width | 40)
| | Sample_data_processing | > Pset <- fitPLM(RK111904_CELs)
| | Sample_data_processing = > image(Pset, which = 1, type | "sign.resids")
| | Sample_data_processing | > ...
| | Sample_data_processing = > RLE(Pset, main = "RLE for RK111904_CELs", ylim | c(-6,7))
| | Sample_data_processing = > NUSE(Pset, main = "NUSE for RK111904_CELs", ylim | c(0.85,1.5))
| | Sample_data_processing | ######################
| | Sample_data_processing | ### Pre-processing ###
| | Sample_data_processing | # Background correction, normalization, PM correction, and summarization
| | Sample_data_processing | > RK111904_fullEset <- expresso(RK111904_CELs,bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish")
| | Sample_data_processing | The quality-control step did not uncover notable defects other than a higher background level in file 154_E.CEL, which was corrected in the pre-processing step. For each sample, the paired Affymetrix probe-set IDs (ID_REF) and pre-processed expression levels (VALUE) were then exported as text files.
| | Sample_data_processing | Reference: Gentleman R., Huber W., Carey V.J., Irizarry R., Smith C., Zhang J., Li X., Scholtens D., Ding B., and Dudoit S. (eds). Bioinformatics and Computational Biology Solutions Using R and Bioconductor. London: Springer. 2005.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Richard,,Kollmar
| | Sample_contact_institute | University of Illinois at Urbana-Champaign
| | Sample_contact_address | 407 S. Goodwin Ave., MC-114
| | Sample_contact_city | Urbana
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 61801
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM321nnn/GSM321745/suppl/GSM321745.CEL.gz
| | Sample_series_id | GSE12810
| | Sample_data_row_count | 45101
| | |
|
GSM321746 | GPL1261 |
|
Modioli_negative-control_rep1
|
Left and right cochlear modiolus, not noise-exposed, animal '8A'
|
aliases: '152', '8A'
biological replicate: 1 of 3
strain: CBA/CaJ
gender: male
date of birth: 7/22/2004
litter number: 8
individual number: 1
date of noise exposure: n/a
date of sacrifice: 9/16/2004
tissue: left and right modioli dissected from cochlea
total rna: 21 ng
amplified cdna: 6.4 micrograms
fragmented and biotinylated cdna: 5.1 micrograms
|
n/a
|
| Sample_geo_accession | GSM321746
| | Sample_status | Public on Sep 16 2009
| | Sample_submission_date | Sep 17 2008
| | Sample_last_update_date | Feb 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Laboratories of Drs. Albert S. Feng and Richard Kollmar
| | Sample_treatment_protocol_ch1 | At four weeks of age, 'treated' animals were exposed together for five hours to two-octave band-limited noise (5-20 kHz) at 110 dB SPL. The animals were distributed between two empty 10-gallon glass tanks inside an acoustic isolation chamber in a separate room. A model S81-02 noise generator (Coulbourn, Whitehall, PA), a model GFP-555II preamplifier (Adcom, Scottsdale, AZ), and a model XL-600 power amplifier (Hafler, Tempe, AZ) drove one model 100HT high-efficiency horn tweeter with a flat frequency response from 2 to 20 kHz (Fostex, Boonton, NJ) over each tank. The noise level was monitored with a model 2239 sound level meter (Brüel & Kjær, Nærum, Denmark). The animals' behavior did not change during the noise exposure. 'Untreated' (negative-control) animals remained in the holding room throughout the experiment and were not exposed to elevated noise levels.
| | Sample_growth_protocol_ch1 | Noise-exposed and negative-control animals were kept next to each other in the same holding room of the animal facility at the Beckman Institute and maintained according to standard procedures. All experiments were conducted in accordance with protocols approved by the University of Illinois Institutional Animal Care and Use Committee.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Both treated and untreated animals were sacrificed at 8 weeks of age. Modioli were rapidly dissected in physiological saline (within 8 min after sacrifice), dissolved in Trizol (Invitrogen, Carlsbad, CA) with a small rotor-stator homogenizer (Tissue-Tearor; Biospec Products, Bartlesville, OK), and stored at -80°C. Total RNA was extracted from all samples in parallel, with glycogen added to maximize precipitation. The resuspended RNA was further purified by adsorption to silica-gel-membrane spin columns (RNeasy MinElute Cleanup kit; Qiagen, Valencia, CA) and eluted in a minimal volume of water. The concentration of the RNA was determined by fluorometry (RiboGreen; Invitrogen), and its integrity was confirmed by electrophoresis (2100 Bioanalyzer; Agilent, Santa Clara, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The entire RNA sample was reverse transcribed, linearly amplified, fragmented, and biotinylated with an Ovation Biotin kit version 1.0 (NuGEN, San Carlos, CA). The cDNA concentrations after amplification and labeling were determined by spectrophotometry.
| | Sample_hyb_protocol | The biotinylated cDNA was hybridized to a Mouse Expression Set 430 2.0 array in a Hybridization Oven 640 (Affymetrix, Santa Clara, CA). After 16 hours, the array was stained and washed in a Fluidics Station 450 (Affymetrix) according to protocol EukGE-WS2v4_450.
| | Sample_scan_protocol | The stained array was imaged in a Gene Chip Scanner 3000 (Affymetrix)
| | Sample_scan_protocol | at a resolution of 1.56 µm per pixel and a wavelength of 570 nm. The probe hybridization signals (cell intensity data) were extracted from the .DAT image file with Affymetrix software and saved as a .CEL file. Both hybridization and scan steps were performed at the Roy J. Carver Biotechnology Center of the University of Illinois at Urbana-Champaign.
| | Sample_data_processing | The probe hybridization signals of all six samples (files 149_E.CEL to 154_E.CEL) were pre-processed together with Bioconductor tools (release 2.1; www.bioconductor.org) in R software (version 2.6.1; http://www.r-project.org) according to the procedures outlined in Gentleman et al. (2005) by using the following commands:
| | Sample_data_processing | #################
| | Sample_data_processing | ### Importing ###
| | Sample_data_processing | # import .CEL files in working directory into Affybatch object RK111904_CELs
| | Sample_data_processing | > library("affy")
| | Sample_data_processing | > RK111904_CELs <- ReadAffy()
| | Sample_data_processing | #######################
| | Sample_data_processing | ### Quality Control ###
| | Sample_data_processing | # Simple and Affymetrix-style quality control of hybridization data
| | Sample_data_processing | > library(affyQCReport)
| | Sample_data_processing | > QCReport(RK111904_CELs,file="affyQCReport.pdf")
| | Sample_data_processing | # Check for RNA degradation
| | Sample_data_processing | > RNAdeg <- AffyRNAdeg(RK111904_CELs)
| | Sample_data_processing = > plotAffyRNAdeg(RNAdeg, col | c(2,3,2,3,3,2))
| | Sample_data_processing | > summaryAffyRNAdeg(RNAdeg)
| | Sample_data_processing | # Check for abnormal population distributions of hybridization signals
| | Sample_data_processing | > library(geneplotter)
| | Sample_data_processing = > MAplot(RK111904_CELs,pairs=TRUE,plot.method="smoothScatter", cex | 1.2)
| | Sample_data_processing | # Check for abnormal spatial distributions of hybridization signals
| | Sample_data_processing | > library(affyPLM)
| | Sample_data_processing = > options(width | 40)
| | Sample_data_processing | > Pset <- fitPLM(RK111904_CELs)
| | Sample_data_processing = > image(Pset, which = 1, type | "sign.resids")
| | Sample_data_processing | > ...
| | Sample_data_processing = > RLE(Pset, main = "RLE for RK111904_CELs", ylim | c(-6,7))
| | Sample_data_processing = > NUSE(Pset, main = "NUSE for RK111904_CELs", ylim | c(0.85,1.5))
| | Sample_data_processing | ######################
| | Sample_data_processing | ### Pre-processing ###
| | Sample_data_processing | # Background correction, normalization, PM correction, and summarization
| | Sample_data_processing | > RK111904_fullEset <- expresso(RK111904_CELs,bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish")
| | Sample_data_processing | The quality-control step did not uncover notable defects other than a higher background level in file 154_E.CEL, which was corrected in the pre-processing step. For each sample, the paired Affymetrix probe-set IDs (ID_REF) and pre-processed expression levels (VALUE) were then exported as text files.
| | Sample_data_processing | Reference: Gentleman R., Huber W., Carey V.J., Irizarry R., Smith C., Zhang J., Li X., Scholtens D., Ding B., and Dudoit S. (eds). Bioinformatics and Computational Biology Solutions Using R and Bioconductor. London: Springer. 2005.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Richard,,Kollmar
| | Sample_contact_institute | University of Illinois at Urbana-Champaign
| | Sample_contact_address | 407 S. Goodwin Ave., MC-114
| | Sample_contact_city | Urbana
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 61801
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM321nnn/GSM321746/suppl/GSM321746.CEL.gz
| | Sample_series_id | GSE12810
| | Sample_data_row_count | 45101
| | |
|
GSM321747 | GPL1261 |
|
Modioli_negative-control_rep2
|
Left and right cochlear modiolus, not noise-exposed, animal '10-1'
|
aliases: '153', '10-1'
biological replicate: 2 of 3
strain: CBA/CaJ
gender: female
date of birth: 7/28/2004
litter number: 10
individual number: 1
date of noise exposure: n/a
date of sacrifice: 9/25/2004
tissue: left and right modioli dissected from cochlea
total rna: 8 ng
amplified cdna: 5.2 micrograms
fragmented and biotinylated cdna: 3.5 micrograms
|
n/a
|
| Sample_geo_accession | GSM321747
| | Sample_status | Public on Sep 16 2009
| | Sample_submission_date | Sep 17 2008
| | Sample_last_update_date | Feb 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Laboratories of Drs. Albert S. Feng and Richard Kollmar
| | Sample_treatment_protocol_ch1 | At four weeks of age, 'treated' animals were exposed together for five hours to two-octave band-limited noise (5-20 kHz) at 110 dB SPL. The animals were distributed between two empty 10-gallon glass tanks inside an acoustic isolation chamber in a separate room. A model S81-02 noise generator (Coulbourn, Whitehall, PA), a model GFP-555II preamplifier (Adcom, Scottsdale, AZ), and a model XL-600 power amplifier (Hafler, Tempe, AZ) drove one model 100HT high-efficiency horn tweeter with a flat frequency response from 2 to 20 kHz (Fostex, Boonton, NJ) over each tank. The noise level was monitored with a model 2239 sound level meter (Brüel & Kjær, Nærum, Denmark). The animals' behavior did not change during the noise exposure. 'Untreated' (negative-control) animals remained in the holding room throughout the experiment and were not exposed to elevated noise levels.
| | Sample_growth_protocol_ch1 | Noise-exposed and negative-control animals were kept next to each other in the same holding room of the animal facility at the Beckman Institute and maintained according to standard procedures. All experiments were conducted in accordance with protocols approved by the University of Illinois Institutional Animal Care and Use Committee.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Both treated and untreated animals were sacrificed at 8 weeks of age. Modioli were rapidly dissected in physiological saline (within 8 min after sacrifice), dissolved in Trizol (Invitrogen, Carlsbad, CA) with a small rotor-stator homogenizer (Tissue-Tearor; Biospec Products, Bartlesville, OK), and stored at -80°C. Total RNA was extracted from all samples in parallel, with glycogen added to maximize precipitation. The resuspended RNA was further purified by adsorption to silica-gel-membrane spin columns (RNeasy MinElute Cleanup kit; Qiagen, Valencia, CA) and eluted in a minimal volume of water. The concentration of the RNA was determined by fluorometry (RiboGreen; Invitrogen), and its integrity was confirmed by electrophoresis (2100 Bioanalyzer; Agilent, Santa Clara, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The entire RNA sample was reverse transcribed, linearly amplified, fragmented, and biotinylated with an Ovation Biotin kit version 1.0 (NuGEN, San Carlos, CA). The cDNA concentrations after amplification and labeling were determined by spectrophotometry.
| | Sample_hyb_protocol | The biotinylated cDNA was hybridized to a Mouse Expression Set 430 2.0 array in a Hybridization Oven 640 (Affymetrix, Santa Clara, CA). After 16 hours, the array was stained and washed in a Fluidics Station 450 (Affymetrix) according to protocol EukGE-WS2v4_450.
| | Sample_scan_protocol | The stained array was imaged in a Gene Chip Scanner 3000 (Affymetrix)
| | Sample_scan_protocol | at a resolution of 1.56 µm per pixel and a wavelength of 570 nm. The probe hybridization signals (cell intensity data) were extracted from the .DAT image file with Affymetrix software and saved as a .CEL file. Both hybridization and scan steps were performed at the Roy J. Carver Biotechnology Center of the University of Illinois at Urbana-Champaign.
| | Sample_data_processing | The probe hybridization signals of all six samples (files 149_E.CEL to 154_E.CEL) were pre-processed together with Bioconductor tools (release 2.1; www.bioconductor.org) in R software (version 2.6.1; http://www.r-project.org) according to the procedures outlined in Gentleman et al. (2005) by using the following commands:
| | Sample_data_processing | #################
| | Sample_data_processing | ### Importing ###
| | Sample_data_processing | # import .CEL files in working directory into Affybatch object RK111904_CELs
| | Sample_data_processing | > library("affy")
| | Sample_data_processing | > RK111904_CELs <- ReadAffy()
| | Sample_data_processing | #######################
| | Sample_data_processing | ### Quality Control ###
| | Sample_data_processing | # Simple and Affymetrix-style quality control of hybridization data
| | Sample_data_processing | > library(affyQCReport)
| | Sample_data_processing | > QCReport(RK111904_CELs,file="affyQCReport.pdf")
| | Sample_data_processing | # Check for RNA degradation
| | Sample_data_processing | > RNAdeg <- AffyRNAdeg(RK111904_CELs)
| | Sample_data_processing = > plotAffyRNAdeg(RNAdeg, col | c(2,3,2,3,3,2))
| | Sample_data_processing | > summaryAffyRNAdeg(RNAdeg)
| | Sample_data_processing | # Check for abnormal population distributions of hybridization signals
| | Sample_data_processing | > library(geneplotter)
| | Sample_data_processing = > MAplot(RK111904_CELs,pairs=TRUE,plot.method="smoothScatter", cex | 1.2)
| | Sample_data_processing | # Check for abnormal spatial distributions of hybridization signals
| | Sample_data_processing | > library(affyPLM)
| | Sample_data_processing = > options(width | 40)
| | Sample_data_processing | > Pset <- fitPLM(RK111904_CELs)
| | Sample_data_processing = > image(Pset, which = 1, type | "sign.resids")
| | Sample_data_processing | > ...
| | Sample_data_processing = > RLE(Pset, main = "RLE for RK111904_CELs", ylim | c(-6,7))
| | Sample_data_processing = > NUSE(Pset, main = "NUSE for RK111904_CELs", ylim | c(0.85,1.5))
| | Sample_data_processing | ######################
| | Sample_data_processing | ### Pre-processing ###
| | Sample_data_processing | # Background correction, normalization, PM correction, and summarization
| | Sample_data_processing | > RK111904_fullEset <- expresso(RK111904_CELs,bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish")
| | Sample_data_processing | The quality-control step did not uncover notable defects other than a higher background level in file 154_E.CEL, which was corrected in the pre-processing step. For each sample, the paired Affymetrix probe-set IDs (ID_REF) and pre-processed expression levels (VALUE) were then exported as text files.
| | Sample_data_processing | Reference: Gentleman R., Huber W., Carey V.J., Irizarry R., Smith C., Zhang J., Li X., Scholtens D., Ding B., and Dudoit S. (eds). Bioinformatics and Computational Biology Solutions Using R and Bioconductor. London: Springer. 2005.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Richard,,Kollmar
| | Sample_contact_institute | University of Illinois at Urbana-Champaign
| | Sample_contact_address | 407 S. Goodwin Ave., MC-114
| | Sample_contact_city | Urbana
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 61801
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM321nnn/GSM321747/suppl/GSM321747.CEL.gz
| | Sample_series_id | GSE12810
| | Sample_data_row_count | 45101
| | |
|
GSM321748 | GPL1261 |
|
Modioli_negative-control_rep3
|
Left and right cochlear modiolus, not noise-exposed, animal '11-3'
|
aliases: '154', '11-3'
biological replicate: 3 of 3
strain: CBA/CaJ
gender: male
date of birth: 8/3/2004
litter number: 11
individual number: 3
date of noise exposure: n/a
date of sacrifice: 9/25/2004
tissue: left and right modioli dissected from cochlea
total rna: 8 ng
amplified cdna: 5.8 micrograms
fragmented and biotinylated cdna: 3.7 micrograms
|
n/a
|
| Sample_geo_accession | GSM321748
| | Sample_status | Public on Sep 16 2009
| | Sample_submission_date | Sep 17 2008
| | Sample_last_update_date | Feb 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Laboratories of Drs. Albert S. Feng and Richard Kollmar
| | Sample_treatment_protocol_ch1 | At four weeks of age, 'treated' animals were exposed together for five hours to two-octave band-limited noise (5-20 kHz) at 110 dB SPL. The animals were distributed between two empty 10-gallon glass tanks inside an acoustic isolation chamber in a separate room. A model S81-02 noise generator (Coulbourn, Whitehall, PA), a model GFP-555II preamplifier (Adcom, Scottsdale, AZ), and a model XL-600 power amplifier (Hafler, Tempe, AZ) drove one model 100HT high-efficiency horn tweeter with a flat frequency response from 2 to 20 kHz (Fostex, Boonton, NJ) over each tank. The noise level was monitored with a model 2239 sound level meter (Brüel & Kjær, Nærum, Denmark). The animals' behavior did not change during the noise exposure. 'Untreated' (negative-control) animals remained in the holding room throughout the experiment and were not exposed to elevated noise levels.
| | Sample_growth_protocol_ch1 | Noise-exposed and negative-control animals were kept next to each other in the same holding room of the animal facility at the Beckman Institute and maintained according to standard procedures. All experiments were conducted in accordance with protocols approved by the University of Illinois Institutional Animal Care and Use Committee.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Both treated and untreated animals were sacrificed at 8 weeks of age. Modioli were rapidly dissected in physiological saline (within 8 min after sacrifice), dissolved in Trizol (Invitrogen, Carlsbad, CA) with a small rotor-stator homogenizer (Tissue-Tearor; Biospec Products, Bartlesville, OK), and stored at -80°C. Total RNA was extracted from all samples in parallel, with glycogen added to maximize precipitation. The resuspended RNA was further purified by adsorption to silica-gel-membrane spin columns (RNeasy MinElute Cleanup kit; Qiagen, Valencia, CA) and eluted in a minimal volume of water. The concentration of the RNA was determined by fluorometry (RiboGreen; Invitrogen), and its integrity was confirmed by electrophoresis (2100 Bioanalyzer; Agilent, Santa Clara, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | The entire RNA sample was reverse transcribed, linearly amplified, fragmented, and biotinylated with an Ovation Biotin kit version 1.0 (NuGEN, San Carlos, CA). The cDNA concentrations after amplification and labeling were determined by spectrophotometry.
| | Sample_hyb_protocol | The biotinylated cDNA was hybridized to a Mouse Expression Set 430 2.0 array in a Hybridization Oven 640 (Affymetrix, Santa Clara, CA). After 16 hours, the array was stained and washed in a Fluidics Station 450 (Affymetrix) according to protocol EukGE-WS2v4_450.
| | Sample_scan_protocol | The stained array was imaged in a Gene Chip Scanner 3000 (Affymetrix)
| | Sample_scan_protocol | at a resolution of 1.56 µm per pixel and a wavelength of 570 nm. The probe hybridization signals (cell intensity data) were extracted from the .DAT image file with Affymetrix software and saved as a .CEL file. Both hybridization and scan steps were performed at the Roy J. Carver Biotechnology Center of the University of Illinois at Urbana-Champaign.
| | Sample_data_processing | The probe hybridization signals of all six samples (files 149_E.CEL to 154_E.CEL) were pre-processed together with Bioconductor tools (release 2.1; www.bioconductor.org) in R software (version 2.6.1; http://www.r-project.org) according to the procedures outlined in Gentleman et al. (2005) by using the following commands:
| | Sample_data_processing | #################
| | Sample_data_processing | ### Importing ###
| | Sample_data_processing | # import .CEL files in working directory into Affybatch object RK111904_CELs
| | Sample_data_processing | > library("affy")
| | Sample_data_processing | > RK111904_CELs <- ReadAffy()
| | Sample_data_processing | #######################
| | Sample_data_processing | ### Quality Control ###
| | Sample_data_processing | # Simple and Affymetrix-style quality control of hybridization data
| | Sample_data_processing | > library(affyQCReport)
| | Sample_data_processing | > QCReport(RK111904_CELs,file="affyQCReport.pdf")
| | Sample_data_processing | # Check for RNA degradation
| | Sample_data_processing | > RNAdeg <- AffyRNAdeg(RK111904_CELs)
| | Sample_data_processing = > plotAffyRNAdeg(RNAdeg, col | c(2,3,2,3,3,2))
| | Sample_data_processing | > summaryAffyRNAdeg(RNAdeg)
| | Sample_data_processing | # Check for abnormal population distributions of hybridization signals
| | Sample_data_processing | > library(geneplotter)
| | Sample_data_processing = > MAplot(RK111904_CELs,pairs=TRUE,plot.method="smoothScatter", cex | 1.2)
| | Sample_data_processing | # Check for abnormal spatial distributions of hybridization signals
| | Sample_data_processing | > library(affyPLM)
| | Sample_data_processing = > options(width | 40)
| | Sample_data_processing | > Pset <- fitPLM(RK111904_CELs)
| | Sample_data_processing = > image(Pset, which = 1, type | "sign.resids")
| | Sample_data_processing | > ...
| | Sample_data_processing = > RLE(Pset, main = "RLE for RK111904_CELs", ylim | c(-6,7))
| | Sample_data_processing = > NUSE(Pset, main = "NUSE for RK111904_CELs", ylim | c(0.85,1.5))
| | Sample_data_processing | ######################
| | Sample_data_processing | ### Pre-processing ###
| | Sample_data_processing | # Background correction, normalization, PM correction, and summarization
| | Sample_data_processing | > RK111904_fullEset <- expresso(RK111904_CELs,bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish")
| | Sample_data_processing | The quality-control step did not uncover notable defects other than a higher background level in file 154_E.CEL, which was corrected in the pre-processing step. For each sample, the paired Affymetrix probe-set IDs (ID_REF) and pre-processed expression levels (VALUE) were then exported as text files.
| | Sample_data_processing | Reference: Gentleman R., Huber W., Carey V.J., Irizarry R., Smith C., Zhang J., Li X., Scholtens D., Ding B., and Dudoit S. (eds). Bioinformatics and Computational Biology Solutions Using R and Bioconductor. London: Springer. 2005.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Richard,,Kollmar
| | Sample_contact_institute | University of Illinois at Urbana-Champaign
| | Sample_contact_address | 407 S. Goodwin Ave., MC-114
| | Sample_contact_city | Urbana
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 61801
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM321nnn/GSM321748/suppl/GSM321748.CEL.gz
| | Sample_series_id | GSE12810
| | Sample_data_row_count | 45101
| | |
|
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