Search results for the GEO ID: GSE23668 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM580630 | GPL1355 |
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5_uM_KHS_101
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5_uM_KHS_101
|
strain: Fisher 344
cell type: hippocampal progenitor cells
treatment: 5_uM_KHS_101
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5_uM_KHS_101
|
Sample_geo_accession | GSM580630
| Sample_status | Public on Aug 18 2010
| Sample_submission_date | Aug 17 2010
| Sample_last_update_date | Aug 17 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | Rat NPCs were derived and cultured as described previously by others. After hippocampal cell isolation, the number of dissociated cells was determined and 5 × 105 cells were plated in 60-mm uncoated plates. After overnight incubation (37 °C, 5% CO2, and 95% humidity), the medium was changed and the cells were expanded and maintained in an undifferentiated state on polyornithine- (10 ug/mL in water; Sigma) and laminin-coated (5 ug/mL in PBS; Invitrogen) dishes in DMEM/F12 (Invitrogen) supplemented with N2 (Invitrogen) and basic fibroblast growth factor (bFGF, 20 ng/mL; Invitrogen). For KHS101 and shRNA-induction experiments, early passage cells (passaged no more than six times after hippocampal isolation) were trypsinized and plated at a density of 1,000 cells/cm2 into N2 medium (DMEM/F12 supplemented with N2) containing KHS analogs (e.g., KHS101, KHS92, and NP) at different concentrations (0.5-5 uM) or DMSO(0.1%), RA (1-2 uM), BDNF (100 ng/mL), and/or BMP4 (50-100 ng/mL) for 4 d.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNeasy kits (Qiagen) were used to extract total RNA from DMSO- or compound-treated NPCs. The integrity and concentration of RNA were determined via microfluidic analysis on an Experion instrument (BioRad).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | GeneChip 3' IVT Express kits (Affymetrix) were used to amplify cRNA from 5 ug total RNA.
| Sample_hyb_protocol | Standard Affymetrix protocols were used to process Affymetrix rat genome 230_2 microarrays (Affymetrix).
| Sample_scan_protocol | standard Affymetrix procedures
| Sample_data_processing | CEL files were processed using the "full model" of GCRMA (Wu Z, Irizarry RA: Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol 2005, 12(6):882-893.) and R version 2.6.2. GCRMA and associated packages were downloaded from Bioconductor (www.bioconductor.org). GCRMA output was unlogged.
| Sample_platform_id | GPL1355
| Sample_contact_name | John,R,Walker
| Sample_contact_email | jwalker@gnf.org
| Sample_contact_phone | 858-812-1636
| Sample_contact_laboratory | Genetics Core
| Sample_contact_department |
| Sample_contact_institute | Genomics Institute of the Novartis Research Foundation
| Sample_contact_address | 10675 John Jay Hopkins
| Sample_contact_city | San Diego
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 92121
| Sample_contact_country | USA
| Sample_contact_web_link | http://biogps.gnf.org
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM580nnn/GSM580630/suppl/GSM580630.CEL.gz
| Sample_series_id | GSE23668
| Sample_data_row_count | 31099
| |
|
GSM580631 | GPL1355 |
|
1.7_uM_KHS_101
|
1.7_uM_KHS_101
|
strain: Fisher 344
cell type: hippocampal progenitor cells
treatment: 1.7_uM_KHS_101
|
1.7_uM_KHS_101
|
Sample_geo_accession | GSM580631
| Sample_status | Public on Aug 18 2010
| Sample_submission_date | Aug 17 2010
| Sample_last_update_date | Aug 17 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | Rat NPCs were derived and cultured as described previously by others. After hippocampal cell isolation, the number of dissociated cells was determined and 5 × 105 cells were plated in 60-mm uncoated plates. After overnight incubation (37 °C, 5% CO2, and 95% humidity), the medium was changed and the cells were expanded and maintained in an undifferentiated state on polyornithine- (10 ug/mL in water; Sigma) and laminin-coated (5 ug/mL in PBS; Invitrogen) dishes in DMEM/F12 (Invitrogen) supplemented with N2 (Invitrogen) and basic fibroblast growth factor (bFGF, 20 ng/mL; Invitrogen). For KHS101 and shRNA-induction experiments, early passage cells (passaged no more than six times after hippocampal isolation) were trypsinized and plated at a density of 1,000 cells/cm2 into N2 medium (DMEM/F12 supplemented with N2) containing KHS analogs (e.g., KHS101, KHS92, and NP) at different concentrations (0.5-5 uM) or DMSO(0.1%), RA (1-2 uM), BDNF (100 ng/mL), and/or BMP4 (50-100 ng/mL) for 4 d.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNeasy kits (Qiagen) were used to extract total RNA from DMSO- or compound-treated NPCs. The integrity and concentration of RNA were determined via microfluidic analysis on an Experion instrument (BioRad).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | GeneChip 3' IVT Express kits (Affymetrix) were used to amplify cRNA from 5 ug total RNA.
| Sample_hyb_protocol | Standard Affymetrix protocols were used to process Affymetrix rat genome 230_2 microarrays (Affymetrix).
| Sample_scan_protocol | standard Affymetrix procedures
| Sample_data_processing | CEL files were processed using the "full model" of GCRMA (Wu Z, Irizarry RA: Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol 2005, 12(6):882-893.) and R version 2.6.2. GCRMA and associated packages were downloaded from Bioconductor (www.bioconductor.org). GCRMA output was unlogged.
| Sample_platform_id | GPL1355
| Sample_contact_name | John,R,Walker
| Sample_contact_email | jwalker@gnf.org
| Sample_contact_phone | 858-812-1636
| Sample_contact_laboratory | Genetics Core
| Sample_contact_department |
| Sample_contact_institute | Genomics Institute of the Novartis Research Foundation
| Sample_contact_address | 10675 John Jay Hopkins
| Sample_contact_city | San Diego
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 92121
| Sample_contact_country | USA
| Sample_contact_web_link | http://biogps.gnf.org
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM580nnn/GSM580631/suppl/GSM580631.CEL.gz
| Sample_series_id | GSE23668
| Sample_data_row_count | 31099
| |
|
GSM580632 | GPL1355 |
|
1_uM_retinoic_acid_forskolin_
|
1_uM_retinoic_acid_forskolin
|
strain: Fisher 344
cell type: hippocampal progenitor cells
treatment: 1_uM_retinoic_acid_forskolin
|
1_uM_retinoic_acid_forskolin
|
Sample_geo_accession | GSM580632
| Sample_status | Public on Aug 18 2010
| Sample_submission_date | Aug 17 2010
| Sample_last_update_date | Aug 17 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | Rat NPCs were derived and cultured as described previously by others. After hippocampal cell isolation, the number of dissociated cells was determined and 5 × 105 cells were plated in 60-mm uncoated plates. After overnight incubation (37 °C, 5% CO2, and 95% humidity), the medium was changed and the cells were expanded and maintained in an undifferentiated state on polyornithine- (10 ug/mL in water; Sigma) and laminin-coated (5 ug/mL in PBS; Invitrogen) dishes in DMEM/F12 (Invitrogen) supplemented with N2 (Invitrogen) and basic fibroblast growth factor (bFGF, 20 ng/mL; Invitrogen). For KHS101 and shRNA-induction experiments, early passage cells (passaged no more than six times after hippocampal isolation) were trypsinized and plated at a density of 1,000 cells/cm2 into N2 medium (DMEM/F12 supplemented with N2) containing KHS analogs (e.g., KHS101, KHS92, and NP) at different concentrations (0.5-5 uM) or DMSO(0.1%), RA (1-2 uM), BDNF (100 ng/mL), and/or BMP4 (50-100 ng/mL) for 4 d.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNeasy kits (Qiagen) were used to extract total RNA from DMSO- or compound-treated NPCs. The integrity and concentration of RNA were determined via microfluidic analysis on an Experion instrument (BioRad).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | GeneChip 3' IVT Express kits (Affymetrix) were used to amplify cRNA from 5 ug total RNA.
| Sample_hyb_protocol | Standard Affymetrix protocols were used to process Affymetrix rat genome 230_2 microarrays (Affymetrix).
| Sample_scan_protocol | standard Affymetrix procedures
| Sample_data_processing | CEL files were processed using the "full model" of GCRMA (Wu Z, Irizarry RA: Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol 2005, 12(6):882-893.) and R version 2.6.2. GCRMA and associated packages were downloaded from Bioconductor (www.bioconductor.org). GCRMA output was unlogged.
| Sample_platform_id | GPL1355
| Sample_contact_name | John,R,Walker
| Sample_contact_email | jwalker@gnf.org
| Sample_contact_phone | 858-812-1636
| Sample_contact_laboratory | Genetics Core
| Sample_contact_department |
| Sample_contact_institute | Genomics Institute of the Novartis Research Foundation
| Sample_contact_address | 10675 John Jay Hopkins
| Sample_contact_city | San Diego
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 92121
| Sample_contact_country | USA
| Sample_contact_web_link | http://biogps.gnf.org
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM580nnn/GSM580632/suppl/GSM580632.CEL.gz
| Sample_series_id | GSE23668
| Sample_data_row_count | 31099
| |
|
GSM580633 | GPL1355 |
|
DMSO
|
DMSO
|
strain: Fisher 344
cell type: hippocampal progenitor cells
treatment: DMSO
|
DMSO
|
Sample_geo_accession | GSM580633
| Sample_status | Public on Aug 18 2010
| Sample_submission_date | Aug 17 2010
| Sample_last_update_date | Aug 17 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Rattus norvegicus
| Sample_taxid_ch1 | 10116
| Sample_treatment_protocol_ch1 | Rat NPCs were derived and cultured as described previously by others. After hippocampal cell isolation, the number of dissociated cells was determined and 5 × 105 cells were plated in 60-mm uncoated plates. After overnight incubation (37 °C, 5% CO2, and 95% humidity), the medium was changed and the cells were expanded and maintained in an undifferentiated state on polyornithine- (10 ug/mL in water; Sigma) and laminin-coated (5 ug/mL in PBS; Invitrogen) dishes in DMEM/F12 (Invitrogen) supplemented with N2 (Invitrogen) and basic fibroblast growth factor (bFGF, 20 ng/mL; Invitrogen). For KHS101 and shRNA-induction experiments, early passage cells (passaged no more than six times after hippocampal isolation) were trypsinized and plated at a density of 1,000 cells/cm2 into N2 medium (DMEM/F12 supplemented with N2) containing KHS analogs (e.g., KHS101, KHS92, and NP) at different concentrations (0.5-5 uM) or DMSO(0.1%), RA (1-2 uM), BDNF (100 ng/mL), and/or BMP4 (50-100 ng/mL) for 4 d.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | RNeasy kits (Qiagen) were used to extract total RNA from DMSO- or compound-treated NPCs. The integrity and concentration of RNA were determined via microfluidic analysis on an Experion instrument (BioRad).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | GeneChip 3' IVT Express kits (Affymetrix) were used to amplify cRNA from 5 ug total RNA.
| Sample_hyb_protocol | Standard Affymetrix protocols were used to process Affymetrix rat genome 230_2 microarrays (Affymetrix).
| Sample_scan_protocol | standard Affymetrix procedures
| Sample_data_processing | CEL files were processed using the "full model" of GCRMA (Wu Z, Irizarry RA: Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol 2005, 12(6):882-893.) and R version 2.6.2. GCRMA and associated packages were downloaded from Bioconductor (www.bioconductor.org). GCRMA output was unlogged.
| Sample_platform_id | GPL1355
| Sample_contact_name | John,R,Walker
| Sample_contact_email | jwalker@gnf.org
| Sample_contact_phone | 858-812-1636
| Sample_contact_laboratory | Genetics Core
| Sample_contact_department |
| Sample_contact_institute | Genomics Institute of the Novartis Research Foundation
| Sample_contact_address | 10675 John Jay Hopkins
| Sample_contact_city | San Diego
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 92121
| Sample_contact_country | USA
| Sample_contact_web_link | http://biogps.gnf.org
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM580nnn/GSM580633/suppl/GSM580633.CEL.gz
| Sample_series_id | GSE23668
| Sample_data_row_count | 31099
| |
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