Search results for the GEO ID: GSE27212 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM672358 | GPL1355 |
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polyornithine, biological rep. 1
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Spinal cord dissociated cultures on polyornithine
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strain: Sprague-Dawley
cell type: Spinal cord dissociated cultures
|
|
Sample_geo_accession | GSM672358
| Sample_status | Public on Aug 05 2013
| Sample_submission_date | Feb 10 2011
| Sample_last_update_date | Aug 05 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | Dissociated neurons were plated on polyornithine-covered coverslips (control) or on carbon nanotubes (CNT)-covered coverslips and maintained in culture.
| Sample_growth_protocol_ch1 | Spinal cords from P1-P4 rats were dissected and dissociated spinal cord neurons were obtained by enzymatic and mechanical treatments.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, and purified with the RNeasy Mini kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified with a NanoDrop 1000 spectrophotometer (Thermo Scientific).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | A 100 ng-amount of each total RNA sample was amplified and labeled with the Illumina RNA amplification kit according to manufacturer's instructions.
| Sample_hyb_protocol | Labeled cRNA was hybridized on Affymetrix Rat Genome 230 2.0 Arrays. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).
| Sample_scan_protocol | Arrays were scanned with the GeneChip Scanner 3000 7G. Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS).
| Sample_data_processing | Further data processing was performed with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Prior to statistical analysis, normalized data were then filtered based on Affymetrix detection call so that only probes that had a present call in at least one of the arrays were retained. Probes with intensity values <100 in all arrays were also excluded. Statistical analysis was performed with Rank Product.
| Sample_platform_id | GPL1355
| Sample_contact_name | Paola,,Roncaglia
| Sample_contact_department | Neurobiology
| Sample_contact_institute | SISSA/ISAS (International School for Advanced Studies)
| Sample_contact_address | via Bonomea 265
| Sample_contact_city | Trieste
| Sample_contact_state | TS
| Sample_contact_zip/postal_code | 34136
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672358/suppl/GSM672358.CEL.gz
| Sample_series_id | GSE27212
| Sample_data_row_count | 31099
| |
|
GSM672359 | GPL1355 |
|
polyornithine, biological rep. 2
|
Spinal cord dissociated cultures on polyornithine
|
strain: Sprague-Dawley
cell type: Spinal cord dissociated cultures
|
|
Sample_geo_accession | GSM672359
| Sample_status | Public on Aug 05 2013
| Sample_submission_date | Feb 10 2011
| Sample_last_update_date | Aug 05 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | Dissociated neurons were plated on polyornithine-covered coverslips (control) or on carbon nanotubes (CNT)-covered coverslips and maintained in culture.
| Sample_growth_protocol_ch1 | Spinal cords from P1-P4 rats were dissected and dissociated spinal cord neurons were obtained by enzymatic and mechanical treatments.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, and purified with the RNeasy Mini kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified with a NanoDrop 1000 spectrophotometer (Thermo Scientific).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | A 100 ng-amount of each total RNA sample was amplified and labeled with the Illumina RNA amplification kit according to manufacturer's instructions.
| Sample_hyb_protocol | Labeled cRNA was hybridized on Affymetrix Rat Genome 230 2.0 Arrays. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).
| Sample_scan_protocol | Arrays were scanned with the GeneChip Scanner 3000 7G. Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS).
| Sample_data_processing | Further data processing was performed with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Prior to statistical analysis, normalized data were then filtered based on Affymetrix detection call so that only probes that had a present call in at least one of the arrays were retained. Probes with intensity values <100 in all arrays were also excluded. Statistical analysis was performed with Rank Product.
| Sample_platform_id | GPL1355
| Sample_contact_name | Paola,,Roncaglia
| Sample_contact_department | Neurobiology
| Sample_contact_institute | SISSA/ISAS (International School for Advanced Studies)
| Sample_contact_address | via Bonomea 265
| Sample_contact_city | Trieste
| Sample_contact_state | TS
| Sample_contact_zip/postal_code | 34136
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672359/suppl/GSM672359.CEL.gz
| Sample_series_id | GSE27212
| Sample_data_row_count | 31099
| |
|
GSM672360 | GPL1355 |
|
polyornithine, biological rep. 3
|
Spinal cord dissociated cultures on polyornithine
|
strain: Sprague-Dawley
cell type: Spinal cord dissociated cultures
|
|
Sample_geo_accession | GSM672360
| Sample_status | Public on Aug 05 2013
| Sample_submission_date | Feb 10 2011
| Sample_last_update_date | Aug 05 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | Dissociated neurons were plated on polyornithine-covered coverslips (control) or on carbon nanotubes (CNT)-covered coverslips and maintained in culture.
| Sample_growth_protocol_ch1 | Spinal cords from P1-P4 rats were dissected and dissociated spinal cord neurons were obtained by enzymatic and mechanical treatments.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, and purified with the RNeasy Mini kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified with a NanoDrop 1000 spectrophotometer (Thermo Scientific).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | A 100 ng-amount of each total RNA sample was amplified and labeled with the Illumina RNA amplification kit according to manufacturer's instructions.
| Sample_hyb_protocol | Labeled cRNA was hybridized on Affymetrix Rat Genome 230 2.0 Arrays. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).
| Sample_scan_protocol | Arrays were scanned with the GeneChip Scanner 3000 7G. Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS).
| Sample_data_processing | Further data processing was performed with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Prior to statistical analysis, normalized data were then filtered based on Affymetrix detection call so that only probes that had a present call in at least one of the arrays were retained. Probes with intensity values <100 in all arrays were also excluded. Statistical analysis was performed with Rank Product.
| Sample_platform_id | GPL1355
| Sample_contact_name | Paola,,Roncaglia
| Sample_contact_department | Neurobiology
| Sample_contact_institute | SISSA/ISAS (International School for Advanced Studies)
| Sample_contact_address | via Bonomea 265
| Sample_contact_city | Trieste
| Sample_contact_state | TS
| Sample_contact_zip/postal_code | 34136
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672360/suppl/GSM672360.CEL.gz
| Sample_series_id | GSE27212
| Sample_data_row_count | 31099
| |
|
GSM672361 | GPL1355 |
|
CNT, biological rep. 1
|
Spinal cord dissociated cultures on CNT
|
strain: Sprague-Dawley
cell type: Spinal cord dissociated cultures
|
|
Sample_geo_accession | GSM672361
| Sample_status | Public on Aug 05 2013
| Sample_submission_date | Feb 10 2011
| Sample_last_update_date | Aug 05 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | Dissociated neurons were plated on polyornithine-covered coverslips (control) or on carbon nanotubes (CNT)-covered coverslips and maintained in culture.
| Sample_growth_protocol_ch1 | Spinal cords from P1-P4 rats were dissected and dissociated spinal cord neurons were obtained by enzymatic and mechanical treatments.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, and purified with the RNeasy Mini kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified with a NanoDrop 1000 spectrophotometer (Thermo Scientific).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | A 100 ng-amount of each total RNA sample was amplified and labeled with the Illumina RNA amplification kit according to manufacturer's instructions.
| Sample_hyb_protocol | Labeled cRNA was hybridized on Affymetrix Rat Genome 230 2.0 Arrays. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).
| Sample_scan_protocol | Arrays were scanned with the GeneChip Scanner 3000 7G. Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS).
| Sample_data_processing | Further data processing was performed with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Prior to statistical analysis, normalized data were then filtered based on Affymetrix detection call so that only probes that had a present call in at least one of the arrays were retained. Probes with intensity values <100 in all arrays were also excluded. Statistical analysis was performed with Rank Product.
| Sample_platform_id | GPL1355
| Sample_contact_name | Paola,,Roncaglia
| Sample_contact_department | Neurobiology
| Sample_contact_institute | SISSA/ISAS (International School for Advanced Studies)
| Sample_contact_address | via Bonomea 265
| Sample_contact_city | Trieste
| Sample_contact_state | TS
| Sample_contact_zip/postal_code | 34136
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672361/suppl/GSM672361.CEL.gz
| Sample_series_id | GSE27212
| Sample_data_row_count | 31099
| |
|
GSM672362 | GPL1355 |
|
CNT, biological rep. 2
|
Spinal cord dissociated cultures on CNT
|
strain: Sprague-Dawley
cell type: Spinal cord dissociated cultures
|
|
Sample_geo_accession | GSM672362
| Sample_status | Public on Aug 05 2013
| Sample_submission_date | Feb 10 2011
| Sample_last_update_date | Aug 05 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | Dissociated neurons were plated on polyornithine-covered coverslips (control) or on carbon nanotubes (CNT)-covered coverslips and maintained in culture.
| Sample_growth_protocol_ch1 | Spinal cords from P1-P4 rats were dissected and dissociated spinal cord neurons were obtained by enzymatic and mechanical treatments.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, and purified with the RNeasy Mini kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified with a NanoDrop 1000 spectrophotometer (Thermo Scientific).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | A 100 ng-amount of each total RNA sample was amplified and labeled with the Illumina RNA amplification kit according to manufacturer's instructions.
| Sample_hyb_protocol | Labeled cRNA was hybridized on Affymetrix Rat Genome 230 2.0 Arrays. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).
| Sample_scan_protocol | Arrays were scanned with the GeneChip Scanner 3000 7G. Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS).
| Sample_data_processing | Further data processing was performed with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Prior to statistical analysis, normalized data were then filtered based on Affymetrix detection call so that only probes that had a present call in at least one of the arrays were retained. Probes with intensity values <100 in all arrays were also excluded. Statistical analysis was performed with Rank Product.
| Sample_platform_id | GPL1355
| Sample_contact_name | Paola,,Roncaglia
| Sample_contact_department | Neurobiology
| Sample_contact_institute | SISSA/ISAS (International School for Advanced Studies)
| Sample_contact_address | via Bonomea 265
| Sample_contact_city | Trieste
| Sample_contact_state | TS
| Sample_contact_zip/postal_code | 34136
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672362/suppl/GSM672362.CEL.gz
| Sample_series_id | GSE27212
| Sample_data_row_count | 31099
| |
|
GSM672363 | GPL1355 |
|
CNT, biological rep. 3
|
Spinal cord dissociated cultures on CNT
|
strain: Sprague-Dawley
cell type: Spinal cord dissociated cultures
|
|
Sample_geo_accession | GSM672363
| Sample_status | Public on Aug 05 2013
| Sample_submission_date | Feb 10 2011
| Sample_last_update_date | Aug 05 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | Dissociated neurons were plated on polyornithine-covered coverslips (control) or on carbon nanotubes (CNT)-covered coverslips and maintained in culture.
| Sample_growth_protocol_ch1 | Spinal cords from P1-P4 rats were dissected and dissociated spinal cord neurons were obtained by enzymatic and mechanical treatments.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, and purified with the RNeasy Mini kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified with a NanoDrop 1000 spectrophotometer (Thermo Scientific).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | A 100 ng-amount of each total RNA sample was amplified and labeled with the Illumina RNA amplification kit according to manufacturer's instructions.
| Sample_hyb_protocol | Labeled cRNA was hybridized on Affymetrix Rat Genome 230 2.0 Arrays. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).
| Sample_scan_protocol | Arrays were scanned with the GeneChip Scanner 3000 7G. Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS).
| Sample_data_processing | Further data processing was performed with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Prior to statistical analysis, normalized data were then filtered based on Affymetrix detection call so that only probes that had a present call in at least one of the arrays were retained. Probes with intensity values <100 in all arrays were also excluded. Statistical analysis was performed with Rank Product.
| Sample_platform_id | GPL1355
| Sample_contact_name | Paola,,Roncaglia
| Sample_contact_department | Neurobiology
| Sample_contact_institute | SISSA/ISAS (International School for Advanced Studies)
| Sample_contact_address | via Bonomea 265
| Sample_contact_city | Trieste
| Sample_contact_state | TS
| Sample_contact_zip/postal_code | 34136
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM672nnn/GSM672363/suppl/GSM672363.CEL.gz
| Sample_series_id | GSE27212
| Sample_data_row_count | 31099
| |
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