Search results for the GEO ID: GSE8318  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM206254 | GPL1355 |
|
control 24h, biological rep1
|
24h control subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with few synapses
|
| Sample_geo_accession | GSM206254
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206254/suppl/GSM206254.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206255 | GPL1355 |
|
cocultured 24h, biological rep1
|
24h cocultured subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with induced synaptogenesis
|
| Sample_geo_accession | GSM206255
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206255/suppl/GSM206255.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206256 | GPL1355 |
|
control 96h, biological rep1
|
96h control subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with few synapses
|
| Sample_geo_accession | GSM206256
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206256/suppl/GSM206256.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206257 | GPL1355 |
|
cocultured 96h, biological rep1
|
96h cocultured subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with induced synaptogenesis
|
| Sample_geo_accession | GSM206257
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206257/suppl/GSM206257.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206258 | GPL1355 |
|
control 24h, biological rep2
|
24h control subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with few synapses
|
| Sample_geo_accession | GSM206258
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206258/suppl/GSM206258.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206259 | GPL1355 |
|
cocultured 24h, biological rep2
|
24h cocultured subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with induced synaptogenesis
|
| Sample_geo_accession | GSM206259
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206259/suppl/GSM206259.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206260 | GPL1355 |
|
control 96h, biological rep2
|
96h control subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with few synapses
|
| Sample_geo_accession | GSM206260
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206260/suppl/GSM206260.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206261 | GPL1355 |
|
cocultured 96h, biological rep2
|
96h cocultured subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with induced synaptogenesis
|
| Sample_geo_accession | GSM206261
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206261/suppl/GSM206261.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206262 | GPL1355 |
|
control 24h, biological rep3
|
24h control subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with few synapses
|
| Sample_geo_accession | GSM206262
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206262/suppl/GSM206262.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206263 | GPL1355 |
|
cocultured 24h, biological rep3
|
24h cocultured subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with induced synaptogenesis
|
| Sample_geo_accession | GSM206263
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206263/suppl/GSM206263.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206264 | GPL1355 |
|
control 96h, biological rep3
|
96h control subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with few synapses
|
| Sample_geo_accession | GSM206264
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206264/suppl/GSM206264.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206265 | GPL1355 |
|
cocultured 96h, biological rep3
|
96h cocultured subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with induced synaptogenesis
|
| Sample_geo_accession | GSM206265
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206265/suppl/GSM206265.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206266 | GPL1355 |
|
control 24h, biological rep4
|
24h control subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with few synapses
|
| Sample_geo_accession | GSM206266
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206266/suppl/GSM206266.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206267 | GPL1355 |
|
cocultured 24h, biological rep4
|
24h cocultured subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with induced synaptogenesis
|
| Sample_geo_accession | GSM206267
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206267/suppl/GSM206267.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206268 | GPL1355 |
|
control 96h, biological rep4
|
96h control subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with few synapses
|
| Sample_geo_accession | GSM206268
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206268/suppl/GSM206268.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206269 | GPL1355 |
|
cocultured 96h, biological rep4
|
96h cocultured subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with induced synaptogenesis
|
| Sample_geo_accession | GSM206269
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206269/suppl/GSM206269.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206270 | GPL1355 |
|
control 24h, biological rep5
|
24h control subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with few synapses
|
| Sample_geo_accession | GSM206270
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206270/suppl/GSM206270.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206271 | GPL1355 |
|
cocultured 24h, biological rep5
|
24h cocultured subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with induced synaptogenesis
|
| Sample_geo_accession | GSM206271
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206271/suppl/GSM206271.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206272 | GPL1355 |
|
control 96h, biological rep5
|
96h control subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with few synapses
|
| Sample_geo_accession | GSM206272
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206272/suppl/GSM206272.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
GSM206273 | GPL1355 |
|
cocultured 96h, biological rep5
|
96h cocultured subplate neurons
|
subplate neurons immunopurified from E17 rats
cultured for 5d before treatment
|
Gene expression data from subplate neurons with induced synaptogenesis
|
| Sample_geo_accession | GSM206273
| | Sample_status | Public on Nov 24 2008
| | Sample_submission_date | Jun 28 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin. Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture. Control feeder wells contained wax dots and media, but no cells. Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.). 24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.
| | Sample_growth_protocol_ch1 | The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells. The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1. Non-adherent cells were washed off and saved to create cortical feeder layers. Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well. Coverslips were coated with poly-ornithine and fibronectin. Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.
| | Sample_data_processing | Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings. Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level. Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Claire,,McKellar
| | Sample_contact_institute | HHMI Janelia Farm Research Campus
| | Sample_contact_address | 19700 Helix Drive
| | Sample_contact_city | Ashburn
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 20147
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM206nnn/GSM206273/suppl/GSM206273.CEL.gz
| | Sample_series_id | GSE8318
| | Sample_data_row_count | 31099
| | |
|
| |
| |
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