Search results for the GEO ID: GSE11730  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM297670 | GPL1355 |
|
axons_naive_13div_1
|
cortical axons, uninjured
|
E18 dissociated cortical and hippocampal neurons, cultured 13 days
|
axons isolated in compartmentalized microfluidic platform
|
| Sample_geo_accession | GSM297670
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Jun 10 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Axons from samples 8-10 were axotomized after 11 days in culture.
| | Sample_growth_protocol_ch1 | Neurobasal E medium supplemented with B27
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Cellular material from 3 microfluidic platforms were pooled for each Genechip sample. RNA was isolated using Ambion RNAqueous®-Micro kit. Isolated RNA underwent 2 rounds of amplification using an Ambion MessageAmp™ II aRNA kit (Austin, TX).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The 2nd round of amplification using the Ambion MessageAmp™ II aRNA kit included biotin-labeling for the GeneChip® hybridization.
| | Sample_hyb_protocol | 15ug of the biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual). Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on the Affymetrix arrays. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol = Genechips were scanned on a GeneChip® Scanner 3000. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity | 500; Normalization, All Probe Sets; Parameters, all set at default values).
| | Sample_data_processing | Expression values were derived from the CEL image files using the robust multi-array average (RMA) algorithm using GeneSpring software (Agilent Technologies, CA). Batch normalized to axonal controls (sample 1-7).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anne,M,Taylor
| | Sample_contact_email | amtaylor@caltech.edu
| | Sample_contact_phone | 626-395-2140
| | Sample_contact_institute | Caltech
| | Sample_contact_address | M/C 114-96
| | Sample_contact_city | Pasadena
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 91125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297670/suppl/GSM297670.CEL.gz
| | Sample_series_id | GSE11730
| | Sample_data_row_count | 31099
| | |
|
GSM297671 | GPL1355 |
|
axons_naive_13div_2
|
cortical axons, uninjured
|
E18 dissociated cortical and hippocampal neurons, cultured 13 days
|
axons isolated in compartmentalized microfluidic platform
|
| Sample_geo_accession | GSM297671
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Jun 10 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Axons from samples 8-10 were axotomized after 11 days in culture.
| | Sample_growth_protocol_ch1 | Neurobasal E medium supplemented with B27
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Cellular material from 3 microfluidic platforms were pooled for each Genechip sample. RNA was isolated using Ambion RNAqueous®-Micro kit. Isolated RNA underwent 2 rounds of amplification using an Ambion MessageAmp™ II aRNA kit (Austin, TX).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The 2nd round of amplification using the Ambion MessageAmp™ II aRNA kit included biotin-labeling for the GeneChip® hybridization.
| | Sample_hyb_protocol | 15ug of the biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual). Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on the Affymetrix arrays. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol = Genechips were scanned on a GeneChip® Scanner 3000. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity | 500; Normalization, All Probe Sets; Parameters, all set at default values).
| | Sample_data_processing | Expression values were derived from the CEL image files using the robust multi-array average (RMA) algorithm using GeneSpring software (Agilent Technologies, CA). Batch normalized to axonal controls (sample 1-7).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anne,M,Taylor
| | Sample_contact_email | amtaylor@caltech.edu
| | Sample_contact_phone | 626-395-2140
| | Sample_contact_institute | Caltech
| | Sample_contact_address | M/C 114-96
| | Sample_contact_city | Pasadena
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 91125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297671/suppl/GSM297671.CEL.gz
| | Sample_series_id | GSE11730
| | Sample_data_row_count | 31099
| | |
|
GSM297672 | GPL1355 |
|
axons_naive_13div_3
|
cortical axons, uninjured
|
E18 dissociated cortical and hippocampal neurons, cultured 13 days
|
axons isolated in compartmentalized microfluidic platform
|
| Sample_geo_accession | GSM297672
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Jun 10 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Axons from samples 8-10 were axotomized after 11 days in culture.
| | Sample_growth_protocol_ch1 | Neurobasal E medium supplemented with B27
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Cellular material from 3 microfluidic platforms were pooled for each Genechip sample. RNA was isolated using Ambion RNAqueous®-Micro kit. Isolated RNA underwent 2 rounds of amplification using an Ambion MessageAmp™ II aRNA kit (Austin, TX).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The 2nd round of amplification using the Ambion MessageAmp™ II aRNA kit included biotin-labeling for the GeneChip® hybridization.
| | Sample_hyb_protocol | 15ug of the biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual). Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on the Affymetrix arrays. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol = Genechips were scanned on a GeneChip® Scanner 3000. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity | 500; Normalization, All Probe Sets; Parameters, all set at default values).
| | Sample_data_processing | Expression values were derived from the CEL image files using the robust multi-array average (RMA) algorithm using GeneSpring software (Agilent Technologies, CA). Batch normalized to axonal controls (sample 1-7).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anne,M,Taylor
| | Sample_contact_email | amtaylor@caltech.edu
| | Sample_contact_phone | 626-395-2140
| | Sample_contact_institute | Caltech
| | Sample_contact_address | M/C 114-96
| | Sample_contact_city | Pasadena
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 91125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297672/suppl/GSM297672.CEL.gz
| | Sample_series_id | GSE11730
| | Sample_data_row_count | 31099
| | |
|
GSM297673 | GPL1355 |
|
axons_naive_13div_4
|
cortical axons, uninjured
|
E18 dissociated cortical and hippocampal neurons, cultured 13 days
|
axons isolated in compartmentalized microfluidic platform
|
| Sample_geo_accession | GSM297673
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Jun 10 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Axons from samples 8-10 were axotomized after 11 days in culture.
| | Sample_growth_protocol_ch1 | Neurobasal E medium supplemented with B27
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Cellular material from 3 microfluidic platforms were pooled for each Genechip sample. RNA was isolated using Ambion RNAqueous®-Micro kit. Isolated RNA underwent 2 rounds of amplification using an Ambion MessageAmp™ II aRNA kit (Austin, TX).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The 2nd round of amplification using the Ambion MessageAmp™ II aRNA kit included biotin-labeling for the GeneChip® hybridization.
| | Sample_hyb_protocol | 15ug of the biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual). Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on the Affymetrix arrays. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol = Genechips were scanned on a GeneChip® Scanner 3000. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity | 500; Normalization, All Probe Sets; Parameters, all set at default values).
| | Sample_data_processing | Expression values were derived from the CEL image files using the robust multi-array average (RMA) algorithm using GeneSpring software (Agilent Technologies, CA). Batch normalized to axonal controls (sample 1-7).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anne,M,Taylor
| | Sample_contact_email | amtaylor@caltech.edu
| | Sample_contact_phone | 626-395-2140
| | Sample_contact_institute | Caltech
| | Sample_contact_address | M/C 114-96
| | Sample_contact_city | Pasadena
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 91125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297673/suppl/GSM297673.CEL.gz
| | Sample_series_id | GSE11730
| | Sample_data_row_count | 31099
| | |
|
GSM297674 | GPL1355 |
|
axons_naive_13div_5
|
cortical axons, uninjured
|
E18 dissociated cortical and hippocampal neurons, cultured 13 days
|
axons isolated in compartmentalized microfluidic platform
|
| Sample_geo_accession | GSM297674
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Jun 10 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Axons from samples 8-10 were axotomized after 11 days in culture.
| | Sample_growth_protocol_ch1 | Neurobasal E medium supplemented with B27
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Cellular material from 3 microfluidic platforms were pooled for each Genechip sample. RNA was isolated using Ambion RNAqueous®-Micro kit. Isolated RNA underwent 2 rounds of amplification using an Ambion MessageAmp™ II aRNA kit (Austin, TX).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The 2nd round of amplification using the Ambion MessageAmp™ II aRNA kit included biotin-labeling for the GeneChip® hybridization.
| | Sample_hyb_protocol | 15ug of the biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual). Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on the Affymetrix arrays. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol = Genechips were scanned on a GeneChip® Scanner 3000. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity | 500; Normalization, All Probe Sets; Parameters, all set at default values).
| | Sample_data_processing | Expression values were derived from the CEL image files using the robust multi-array average (RMA) algorithm using GeneSpring software (Agilent Technologies, CA). Batch normalized to axonal controls (sample 1-7).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anne,M,Taylor
| | Sample_contact_email | amtaylor@caltech.edu
| | Sample_contact_phone | 626-395-2140
| | Sample_contact_institute | Caltech
| | Sample_contact_address | M/C 114-96
| | Sample_contact_city | Pasadena
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 91125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297674/suppl/GSM297674.CEL.gz
| | Sample_series_id | GSE11730
| | Sample_data_row_count | 31099
| | |
|
GSM297675 | GPL1355 |
|
axons_naive_13div_6
|
cortical axons, uninjured
|
E18 dissociated cortical and hippocampal neurons, cultured 13 days
|
axons isolated in compartmentalized microfluidic platform
|
| Sample_geo_accession | GSM297675
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Jun 10 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Axons from samples 8-10 were axotomized after 11 days in culture.
| | Sample_growth_protocol_ch1 | Neurobasal E medium supplemented with B27
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Cellular material from 3 microfluidic platforms were pooled for each Genechip sample. RNA was isolated using Ambion RNAqueous®-Micro kit. Isolated RNA underwent 2 rounds of amplification using an Ambion MessageAmp™ II aRNA kit (Austin, TX).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The 2nd round of amplification using the Ambion MessageAmp™ II aRNA kit included biotin-labeling for the GeneChip® hybridization.
| | Sample_hyb_protocol | 15ug of the biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual). Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on the Affymetrix arrays. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol = Genechips were scanned on a GeneChip® Scanner 3000. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity | 500; Normalization, All Probe Sets; Parameters, all set at default values).
| | Sample_data_processing | Expression values were derived from the CEL image files using the robust multi-array average (RMA) algorithm using GeneSpring software (Agilent Technologies, CA). Batch normalized to axonal controls (sample 1-7).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anne,M,Taylor
| | Sample_contact_email | amtaylor@caltech.edu
| | Sample_contact_phone | 626-395-2140
| | Sample_contact_institute | Caltech
| | Sample_contact_address | M/C 114-96
| | Sample_contact_city | Pasadena
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 91125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297675/suppl/GSM297675.CEL.gz
| | Sample_series_id | GSE11730
| | Sample_data_row_count | 31099
| | |
|
GSM297676 | GPL1355 |
|
axons_naive_13div_7
|
cortical axons, uninjured
|
E18 dissociated cortical and hippocampal neurons, cultured 13 days
|
axons isolated in compartmentalized microfluidic platform
|
| Sample_geo_accession | GSM297676
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Jun 10 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Axons from samples 8-10 were axotomized after 11 days in culture.
| | Sample_growth_protocol_ch1 | Neurobasal E medium supplemented with B27
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Cellular material from 3 microfluidic platforms were pooled for each Genechip sample. RNA was isolated using Ambion RNAqueous®-Micro kit. Isolated RNA underwent 2 rounds of amplification using an Ambion MessageAmp™ II aRNA kit (Austin, TX).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The 2nd round of amplification using the Ambion MessageAmp™ II aRNA kit included biotin-labeling for the GeneChip® hybridization.
| | Sample_hyb_protocol | 15ug of the biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual). Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on the Affymetrix arrays. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol = Genechips were scanned on a GeneChip® Scanner 3000. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity | 500; Normalization, All Probe Sets; Parameters, all set at default values).
| | Sample_data_processing | Expression values were derived from the CEL image files using the robust multi-array average (RMA) algorithm using GeneSpring software (Agilent Technologies, CA). Batch normalized to axonal controls (sample 1-7).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anne,M,Taylor
| | Sample_contact_email | amtaylor@caltech.edu
| | Sample_contact_phone | 626-395-2140
| | Sample_contact_institute | Caltech
| | Sample_contact_address | M/C 114-96
| | Sample_contact_city | Pasadena
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 91125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297676/suppl/GSM297676.CEL.gz
| | Sample_series_id | GSE11730
| | Sample_data_row_count | 31099
| | |
|
GSM297677 | GPL1355 |
|
axons_regen_13div_1
|
cortical axons, 2 days after axotomy
|
E18 dissociated cortical and hippocampal neurons, cultured 13 days
|
axons isolated in compartmentalized microfluidic platform
|
| Sample_geo_accession | GSM297677
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Jun 10 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Axons from samples 8-10 were axotomized after 11 days in culture.
| | Sample_growth_protocol_ch1 | Neurobasal E medium supplemented with B27
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Cellular material from 3 microfluidic platforms were pooled for each Genechip sample. RNA was isolated using Ambion RNAqueous®-Micro kit. Isolated RNA underwent 2 rounds of amplification using an Ambion MessageAmp™ II aRNA kit (Austin, TX).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The 2nd round of amplification using the Ambion MessageAmp™ II aRNA kit included biotin-labeling for the GeneChip® hybridization.
| | Sample_hyb_protocol | 15ug of the biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual). Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on the Affymetrix arrays. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol = Genechips were scanned on a GeneChip® Scanner 3000. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity | 500; Normalization, All Probe Sets; Parameters, all set at default values).
| | Sample_data_processing | Expression values were derived from the CEL image files using the robust multi-array average (RMA) algorithm using GeneSpring software (Agilent Technologies, CA). Batch normalized to axonal controls (sample 1-7).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anne,M,Taylor
| | Sample_contact_email | amtaylor@caltech.edu
| | Sample_contact_phone | 626-395-2140
| | Sample_contact_institute | Caltech
| | Sample_contact_address | M/C 114-96
| | Sample_contact_city | Pasadena
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 91125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297677/suppl/GSM297677.CEL.gz
| | Sample_series_id | GSE11730
| | Sample_data_row_count | 31099
| | |
|
GSM297678 | GPL1355 |
|
axons_regen_13div_2
|
cortical axons, 2 days after axotomy
|
E18 dissociated cortical and hippocampal neurons, cultured 13 days
|
axons isolated in compartmentalized microfluidic platform
|
| Sample_geo_accession | GSM297678
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Jun 10 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Axons from samples 8-10 were axotomized after 11 days in culture.
| | Sample_growth_protocol_ch1 | Neurobasal E medium supplemented with B27
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Cellular material from 3 microfluidic platforms were pooled for each Genechip sample. RNA was isolated using Ambion RNAqueous®-Micro kit. Isolated RNA underwent 2 rounds of amplification using an Ambion MessageAmp™ II aRNA kit (Austin, TX).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The 2nd round of amplification using the Ambion MessageAmp™ II aRNA kit included biotin-labeling for the GeneChip® hybridization.
| | Sample_hyb_protocol | 15ug of the biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual). Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on the Affymetrix arrays. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol = Genechips were scanned on a GeneChip® Scanner 3000. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity | 500; Normalization, All Probe Sets; Parameters, all set at default values).
| | Sample_data_processing | Expression values were derived from the CEL image files using the robust multi-array average (RMA) algorithm using GeneSpring software (Agilent Technologies, CA). Batch normalized to axonal controls (sample 1-7).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anne,M,Taylor
| | Sample_contact_email | amtaylor@caltech.edu
| | Sample_contact_phone | 626-395-2140
| | Sample_contact_institute | Caltech
| | Sample_contact_address | M/C 114-96
| | Sample_contact_city | Pasadena
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 91125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297678/suppl/GSM297678.CEL.gz
| | Sample_series_id | GSE11730
| | Sample_data_row_count | 31099
| | |
|
GSM297679 | GPL1355 |
|
axons_regen_13div_3
|
cortical axons, 2 days after axotomy
|
E18 dissociated cortical and hippocampal neurons, cultured 13 days
|
axons isolated in compartmentalized microfluidic platform
|
| Sample_geo_accession | GSM297679
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Jun 10 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Axons from samples 8-10 were axotomized after 11 days in culture.
| | Sample_growth_protocol_ch1 | Neurobasal E medium supplemented with B27
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Cellular material from 3 microfluidic platforms were pooled for each Genechip sample. RNA was isolated using Ambion RNAqueous®-Micro kit. Isolated RNA underwent 2 rounds of amplification using an Ambion MessageAmp™ II aRNA kit (Austin, TX).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The 2nd round of amplification using the Ambion MessageAmp™ II aRNA kit included biotin-labeling for the GeneChip® hybridization.
| | Sample_hyb_protocol | 15ug of the biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual). Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on the Affymetrix arrays. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol = Genechips were scanned on a GeneChip® Scanner 3000. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity | 500; Normalization, All Probe Sets; Parameters, all set at default values).
| | Sample_data_processing | Expression values were derived from the CEL image files using the robust multi-array average (RMA) algorithm using GeneSpring software (Agilent Technologies, CA). Batch normalized to axonal controls (sample 1-7).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anne,M,Taylor
| | Sample_contact_email | amtaylor@caltech.edu
| | Sample_contact_phone | 626-395-2140
| | Sample_contact_institute | Caltech
| | Sample_contact_address | M/C 114-96
| | Sample_contact_city | Pasadena
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 91125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297679/suppl/GSM297679.CEL.gz
| | Sample_series_id | GSE11730
| | Sample_data_row_count | 31099
| | |
|
GSM297680 | GPL1355 |
|
neurons_naive_13div_1
|
cortical neurons, uninjured
|
E18 dissociated cortical and hippocampal neurons, cultured 13 days
|
neurons isolated in compartmentalized microfluidic platform
|
| Sample_geo_accession | GSM297680
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Jun 10 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Axons from samples 8-10 were axotomized after 11 days in culture.
| | Sample_growth_protocol_ch1 | Neurobasal E medium supplemented with B27
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Cellular material from 3 microfluidic platforms were pooled for each Genechip sample. RNA was isolated using Ambion RNAqueous®-Micro kit. Isolated RNA underwent 2 rounds of amplification using an Ambion MessageAmp™ II aRNA kit (Austin, TX).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The 2nd round of amplification using the Ambion MessageAmp™ II aRNA kit included biotin-labeling for the GeneChip® hybridization.
| | Sample_hyb_protocol | 15ug of the biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual). Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on the Affymetrix arrays. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol = Genechips were scanned on a GeneChip® Scanner 3000. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity | 500; Normalization, All Probe Sets; Parameters, all set at default values).
| | Sample_data_processing | Expression values were derived from the CEL image files using the robust multi-array average (RMA) algorithm using GeneSpring software (Agilent Technologies, CA). Batch normalized to axonal controls (sample 1-7).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anne,M,Taylor
| | Sample_contact_email | amtaylor@caltech.edu
| | Sample_contact_phone | 626-395-2140
| | Sample_contact_institute | Caltech
| | Sample_contact_address | M/C 114-96
| | Sample_contact_city | Pasadena
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 91125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297680/suppl/GSM297680.CEL.gz
| | Sample_series_id | GSE11730
| | Sample_data_row_count | 31099
| | |
|
GSM297681 | GPL1355 |
|
neurons_naive_13div_2
|
cortical neurons, uninjured
|
E18 dissociated cortical and hippocampal neurons, cultured 13 days
|
neurons isolated in compartmentalized microfluidic platform
|
| Sample_geo_accession | GSM297681
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Jun 10 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Axons from samples 8-10 were axotomized after 11 days in culture.
| | Sample_growth_protocol_ch1 | Neurobasal E medium supplemented with B27
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Cellular material from 3 microfluidic platforms were pooled for each Genechip sample. RNA was isolated using Ambion RNAqueous®-Micro kit. Isolated RNA underwent 2 rounds of amplification using an Ambion MessageAmp™ II aRNA kit (Austin, TX).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The 2nd round of amplification using the Ambion MessageAmp™ II aRNA kit included biotin-labeling for the GeneChip® hybridization.
| | Sample_hyb_protocol | 15ug of the biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual). Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on the Affymetrix arrays. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol = Genechips were scanned on a GeneChip® Scanner 3000. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity | 500; Normalization, All Probe Sets; Parameters, all set at default values).
| | Sample_data_processing | Expression values were derived from the CEL image files using the robust multi-array average (RMA) algorithm using GeneSpring software (Agilent Technologies, CA). Batch normalized to axonal controls (sample 1-7).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anne,M,Taylor
| | Sample_contact_email | amtaylor@caltech.edu
| | Sample_contact_phone | 626-395-2140
| | Sample_contact_institute | Caltech
| | Sample_contact_address | M/C 114-96
| | Sample_contact_city | Pasadena
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 91125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297681/suppl/GSM297681.CEL.gz
| | Sample_series_id | GSE11730
| | Sample_data_row_count | 31099
| | |
|
GSM297682 | GPL1355 |
|
neurons_naive_13div_3
|
cortical neurons, uninjured
|
E18 dissociated cortical and hippocampal neurons, cultured 13 days
|
neurons isolated in compartmentalized microfluidic platform
|
| Sample_geo_accession | GSM297682
| | Sample_status | Public on Jan 01 2009
| | Sample_submission_date | Jun 10 2008
| | Sample_last_update_date | Nov 21 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Axons from samples 8-10 were axotomized after 11 days in culture.
| | Sample_growth_protocol_ch1 | Neurobasal E medium supplemented with B27
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Cellular material from 3 microfluidic platforms were pooled for each Genechip sample. RNA was isolated using Ambion RNAqueous®-Micro kit. Isolated RNA underwent 2 rounds of amplification using an Ambion MessageAmp™ II aRNA kit (Austin, TX).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The 2nd round of amplification using the Ambion MessageAmp™ II aRNA kit included biotin-labeling for the GeneChip® hybridization.
| | Sample_hyb_protocol | 15ug of the biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual). Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on the Affymetrix arrays. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.
| | Sample_scan_protocol = Genechips were scanned on a GeneChip® Scanner 3000. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity | 500; Normalization, All Probe Sets; Parameters, all set at default values).
| | Sample_data_processing | Expression values were derived from the CEL image files using the robust multi-array average (RMA) algorithm using GeneSpring software (Agilent Technologies, CA). Batch normalized to axonal controls (sample 1-7).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Anne,M,Taylor
| | Sample_contact_email | amtaylor@caltech.edu
| | Sample_contact_phone | 626-395-2140
| | Sample_contact_institute | Caltech
| | Sample_contact_address | M/C 114-96
| | Sample_contact_city | Pasadena
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 91125
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM297nnn/GSM297682/suppl/GSM297682.CEL.gz
| | Sample_series_id | GSE11730
| | Sample_data_row_count | 31099
| | |
|
| |
| |
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