Result

Search results for the GEO ID: GSE13421

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM338572

GPL1261

normal cochlea rep1

NORMAL COCHLEA

CBA/CaJ, male, 9 weeks, cochlea

none

Sample_geo_accession	GSM338572
Sample_status	Public on Nov 01 2008
Sample_submission_date	Oct 31 2008
Sample_last_update_date	Oct 31 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were given a fatal dose of urethane (300 mg/kg, i.p.) and exsanguinated by cardiac perfusion with sterile saline to remove blood cells from the tissue. Cochleas were collected in RNAlater and the other bony shell of the cochlea was removed with jeweler’s forceps. All soft tissue (spiral ligament, organ of Corti, and modiolus) was collected in RNAlater.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from cochlear soft tissue using Invitrogen's TRIZOL protocol and purified using Qiagen's RNEasy Mini kit in accordance with their standard procedure.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process. The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol.
Sample_hyb_protocol	For each experimental sample, under low quantity conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process. The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol. Quantification of the samples is carried out on a Bio-Tek UV Plate Reader. Hybridization is carried out in an Affymetrix Model 640 hybridization chamber according the Affymetrix GeneChip® Manual. Twenty micrograms of material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
Sample_scan_protocol	Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process. Scanning is carried out on a GeneChip® Model 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred after scanning all samples is completed onto on Partners Healthcare network servers and backed up nightly via the Partners Healthcare Systems IT backup utility.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL1261
Sample_contact_name	Joe,Claud,Adams
Sample_contact_email	Joe_Adams@meei.harvard.edu
Sample_contact_phone	617 5733975
Sample_contact_fax	617 7204408
Sample_contact_laboratory	Eaton-Peabody Lab
Sample_contact_department	Otolaryngology
Sample_contact_institute	Massachusetts Eye & Ear Infirmary
Sample_contact_address	243 Charles St.
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02114
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338572/suppl/GSM338572.CEL.gz
Sample_series_id	GSE13421
Sample_data_row_count	45101

GSM338573

GPL1261

normal cochlea rep2

NORMAL COCHLEA

CBA/CaJ, male, 9 weeks, cochlea

none

Sample_geo_accession	GSM338573
Sample_status	Public on Nov 01 2008
Sample_submission_date	Oct 31 2008
Sample_last_update_date	Oct 31 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were given a fatal dose of urethane (300 mg/kg, i.p.) and exsanguinated by cardiac perfusion with sterile saline to remove blood cells from the tissue. Cochleas were collected in RNAlater and the other bony shell of the cochlea was removed with jeweler’s forceps. All soft tissue (spiral ligament, organ of Corti, and modiolus) was collected in RNAlater.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from cochlear soft tissue using Invitrogen's TRIZOL protocol and purified using Qiagen's RNEasy Mini kit in accordance with their standard procedure.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process. The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol.
Sample_hyb_protocol	For each experimental sample, under low quantity conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process. The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol. Quantification of the samples is carried out on a Bio-Tek UV Plate Reader. Hybridization is carried out in an Affymetrix Model 640 hybridization chamber according the Affymetrix GeneChip® Manual. Twenty micrograms of material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
Sample_scan_protocol	Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process. Scanning is carried out on a GeneChip® Model 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred after scanning all samples is completed onto on Partners Healthcare network servers and backed up nightly via the Partners Healthcare Systems IT backup utility.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL1261
Sample_contact_name	Joe,Claud,Adams
Sample_contact_email	Joe_Adams@meei.harvard.edu
Sample_contact_phone	617 5733975
Sample_contact_fax	617 7204408
Sample_contact_laboratory	Eaton-Peabody Lab
Sample_contact_department	Otolaryngology
Sample_contact_institute	Massachusetts Eye & Ear Infirmary
Sample_contact_address	243 Charles St.
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02114
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338573/suppl/GSM338573.CEL.gz
Sample_series_id	GSE13421
Sample_data_row_count	45101

GSM338574

GPL1261

normal cochlea rep3

NORMAL COCHLEA

CBA/CaJ, male, 9 weeks, cochlea

none

Sample_geo_accession	GSM338574
Sample_status	Public on Nov 01 2008
Sample_submission_date	Oct 31 2008
Sample_last_update_date	Oct 31 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were given a fatal dose of urethane (300 mg/kg, i.p.) and exsanguinated by cardiac perfusion with sterile saline to remove blood cells from the tissue. Cochleas were collected in RNAlater and the other bony shell of the cochlea was removed with jeweler’s forceps. All soft tissue (spiral ligament, organ of Corti, and modiolus) was collected in RNAlater.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from cochlear soft tissue using Invitrogen's TRIZOL protocol and purified using Qiagen's RNEasy Mini kit in accordance with their standard procedure.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process. The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol.
Sample_hyb_protocol	For each experimental sample, under low quantity conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process. The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol. Quantification of the samples is carried out on a Bio-Tek UV Plate Reader. Hybridization is carried out in an Affymetrix Model 640 hybridization chamber according the Affymetrix GeneChip® Manual. Twenty micrograms of material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
Sample_scan_protocol	Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process. Scanning is carried out on a GeneChip® Model 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred after scanning all samples is completed onto on Partners Healthcare network servers and backed up nightly via the Partners Healthcare Systems IT backup utility.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL1261
Sample_contact_name	Joe,Claud,Adams
Sample_contact_email	Joe_Adams@meei.harvard.edu
Sample_contact_phone	617 5733975
Sample_contact_fax	617 7204408
Sample_contact_laboratory	Eaton-Peabody Lab
Sample_contact_department	Otolaryngology
Sample_contact_institute	Massachusetts Eye & Ear Infirmary
Sample_contact_address	243 Charles St.
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02114
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338574/suppl/GSM338574.CEL.gz
Sample_series_id	GSE13421
Sample_data_row_count	45101

GSM338575

GPL1261

normal cochlea rep4

NORMAL COCHLEA

CBA/CaJ, male, 9 weeks, cochlea

none

Sample_geo_accession	GSM338575
Sample_status	Public on Nov 01 2008
Sample_submission_date	Oct 31 2008
Sample_last_update_date	Oct 31 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were given a fatal dose of urethane (300 mg/kg, i.p.) and exsanguinated by cardiac perfusion with sterile saline to remove blood cells from the tissue. Cochleas were collected in RNAlater and the other bony shell of the cochlea was removed with jeweler’s forceps. All soft tissue (spiral ligament, organ of Corti, and modiolus) was collected in RNAlater.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from cochlear soft tissue using Invitrogen's TRIZOL protocol and purified using Qiagen's RNEasy Mini kit in accordance with their standard procedure.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process. The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol.
Sample_hyb_protocol	For each experimental sample, under low quantity conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process. The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol. Quantification of the samples is carried out on a Bio-Tek UV Plate Reader. Hybridization is carried out in an Affymetrix Model 640 hybridization chamber according the Affymetrix GeneChip® Manual. Twenty micrograms of material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
Sample_scan_protocol	Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process. Scanning is carried out on a GeneChip® Model 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred after scanning all samples is completed onto on Partners Healthcare network servers and backed up nightly via the Partners Healthcare Systems IT backup utility.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL1261
Sample_contact_name	Joe,Claud,Adams
Sample_contact_email	Joe_Adams@meei.harvard.edu
Sample_contact_phone	617 5733975
Sample_contact_fax	617 7204408
Sample_contact_laboratory	Eaton-Peabody Lab
Sample_contact_department	Otolaryngology
Sample_contact_institute	Massachusetts Eye & Ear Infirmary
Sample_contact_address	243 Charles St.
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02114
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338575/suppl/GSM338575.CEL.gz
Sample_series_id	GSE13421
Sample_data_row_count	45101

GSM338576

GPL1261

normal cochlea rep5

NORMAL COCHLEA

CBA/CaJ, male, 9 weeks, cochlea

none

Sample_geo_accession	GSM338576
Sample_status	Public on Nov 01 2008
Sample_submission_date	Oct 31 2008
Sample_last_update_date	Oct 31 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were given a fatal dose of urethane (300 mg/kg, i.p.) and exsanguinated by cardiac perfusion with sterile saline to remove blood cells from the tissue. Cochleas were collected in RNAlater and the other bony shell of the cochlea was removed with jeweler’s forceps. All soft tissue (spiral ligament, organ of Corti, and modiolus) was collected in RNAlater.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from cochlear soft tissue using Invitrogen's TRIZOL protocol and purified using Qiagen's RNEasy Mini kit in accordance with their standard procedure.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process. The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol.
Sample_hyb_protocol	For each experimental sample, under low quantity conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process. The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol. Quantification of the samples is carried out on a Bio-Tek UV Plate Reader. Hybridization is carried out in an Affymetrix Model 640 hybridization chamber according the Affymetrix GeneChip® Manual. Twenty micrograms of material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
Sample_scan_protocol	Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process. Scanning is carried out on a GeneChip® Model 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred after scanning all samples is completed onto on Partners Healthcare network servers and backed up nightly via the Partners Healthcare Systems IT backup utility.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL1261
Sample_contact_name	Joe,Claud,Adams
Sample_contact_email	Joe_Adams@meei.harvard.edu
Sample_contact_phone	617 5733975
Sample_contact_fax	617 7204408
Sample_contact_laboratory	Eaton-Peabody Lab
Sample_contact_department	Otolaryngology
Sample_contact_institute	Massachusetts Eye & Ear Infirmary
Sample_contact_address	243 Charles St.
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02114
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338576/suppl/GSM338576.CEL.gz
Sample_series_id	GSE13421
Sample_data_row_count	45101

GSM338577

GPL1261

normal cochlea rep6

NORMAL COCHLEA

CBA/CaJ, male, 9 weeks, cochlea

none

Sample_geo_accession	GSM338577
Sample_status	Public on Nov 01 2008
Sample_submission_date	Oct 31 2008
Sample_last_update_date	Oct 31 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were given a fatal dose of urethane (300 mg/kg, i.p.) and exsanguinated by cardiac perfusion with sterile saline to remove blood cells from the tissue. Cochleas were collected in RNAlater and the other bony shell of the cochlea was removed with jeweler’s forceps. All soft tissue (spiral ligament, organ of Corti, and modiolus) was collected in RNAlater.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from cochlear soft tissue using Invitrogen's TRIZOL protocol and purified using Qiagen's RNEasy Mini kit in accordance with their standard procedure.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process. The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol.
Sample_hyb_protocol	For each experimental sample, under low quantity conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process. The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol. Quantification of the samples is carried out on a Bio-Tek UV Plate Reader. Hybridization is carried out in an Affymetrix Model 640 hybridization chamber according the Affymetrix GeneChip® Manual. Twenty micrograms of material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
Sample_scan_protocol	Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process. Scanning is carried out on a GeneChip® Model 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred after scanning all samples is completed onto on Partners Healthcare network servers and backed up nightly via the Partners Healthcare Systems IT backup utility.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL1261
Sample_contact_name	Joe,Claud,Adams
Sample_contact_email	Joe_Adams@meei.harvard.edu
Sample_contact_phone	617 5733975
Sample_contact_fax	617 7204408
Sample_contact_laboratory	Eaton-Peabody Lab
Sample_contact_department	Otolaryngology
Sample_contact_institute	Massachusetts Eye & Ear Infirmary
Sample_contact_address	243 Charles St.
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02114
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338577/suppl/GSM338577.CEL.gz
Sample_series_id	GSE13421
Sample_data_row_count	45101

GSM338578

GPL1261

normal cochlea rep7

NORMAL COCHLEA

CBA/CaJ, male, 9 weeks, cochlea

none

Sample_geo_accession	GSM338578
Sample_status	Public on Nov 01 2008
Sample_submission_date	Oct 31 2008
Sample_last_update_date	Oct 31 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were given a fatal dose of urethane (300 mg/kg, i.p.) and exsanguinated by cardiac perfusion with sterile saline to remove blood cells from the tissue. Cochleas were collected in RNAlater and the other bony shell of the cochlea was removed with jeweler’s forceps. All soft tissue (spiral ligament, organ of Corti, and modiolus) was collected in RNAlater.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from cochlear soft tissue using Invitrogen's TRIZOL protocol and purified using Qiagen's RNEasy Mini kit in accordance with their standard procedure.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process. The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol.
Sample_hyb_protocol	For each experimental sample, under low quantity conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process. The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol. Quantification of the samples is carried out on a Bio-Tek UV Plate Reader. Hybridization is carried out in an Affymetrix Model 640 hybridization chamber according the Affymetrix GeneChip® Manual. Twenty micrograms of material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
Sample_scan_protocol	Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process. Scanning is carried out on a GeneChip® Model 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred after scanning all samples is completed onto on Partners Healthcare network servers and backed up nightly via the Partners Healthcare Systems IT backup utility.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL1261
Sample_contact_name	Joe,Claud,Adams
Sample_contact_email	Joe_Adams@meei.harvard.edu
Sample_contact_phone	617 5733975
Sample_contact_fax	617 7204408
Sample_contact_laboratory	Eaton-Peabody Lab
Sample_contact_department	Otolaryngology
Sample_contact_institute	Massachusetts Eye & Ear Infirmary
Sample_contact_address	243 Charles St.
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02114
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338578/suppl/GSM338578.CEL.gz
Sample_series_id	GSE13421
Sample_data_row_count	45101

GSM338579

GPL1261

normal cochlea rep8

NORMAL COCHLEA

CBA/CaJ, male, 9 weeks, cochlea

none

Sample_geo_accession	GSM338579
Sample_status	Public on Nov 01 2008
Sample_submission_date	Oct 31 2008
Sample_last_update_date	Oct 31 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were given a fatal dose of urethane (300 mg/kg, i.p.) and exsanguinated by cardiac perfusion with sterile saline to remove blood cells from the tissue. Cochleas were collected in RNAlater and the other bony shell of the cochlea was removed with jeweler’s forceps. All soft tissue (spiral ligament, organ of Corti, and modiolus) was collected in RNAlater.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from cochlear soft tissue using Invitrogen's TRIZOL protocol and purified using Qiagen's RNEasy Mini kit in accordance with their standard procedure.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process. The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol.
Sample_hyb_protocol	For each experimental sample, under low quantity conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Nugen Ovation RNA Amplification System V2. Generation of amplified, antisense single-stranded cDNA is accomplished utilizing a linear isothermal DNA amplification process. The cDNA is then fragmented and labeled following Nugen’s FL-Ovation cDNA Biotin Module V2 protocol. Quantification of the samples is carried out on a Bio-Tek UV Plate Reader. Hybridization is carried out in an Affymetrix Model 640 hybridization chamber according the Affymetrix GeneChip® Manual. Twenty micrograms of material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.
Sample_scan_protocol	Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process. Scanning is carried out on a GeneChip® Model 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred after scanning all samples is completed onto on Partners Healthcare network servers and backed up nightly via the Partners Healthcare Systems IT backup utility.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL1261
Sample_contact_name	Joe,Claud,Adams
Sample_contact_email	Joe_Adams@meei.harvard.edu
Sample_contact_phone	617 5733975
Sample_contact_fax	617 7204408
Sample_contact_laboratory	Eaton-Peabody Lab
Sample_contact_department	Otolaryngology
Sample_contact_institute	Massachusetts Eye & Ear Infirmary
Sample_contact_address	243 Charles St.
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02114
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM338nnn/GSM338579/suppl/GSM338579.CEL.gz
Sample_series_id	GSE13421
Sample_data_row_count	45101

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