Search results for the GEO ID: GSE42565  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1045179 | GPL1261 |
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NEB_RA_rep1
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Neuralized embryoid bodies, all trans retinoic acid (500nM), 3 days
|
tissue: Gli1-FLAG ESC-derived neural progenitors
treatment: all trans retinoic acid (500nM)
|
Neural progenitors were formed by suspension culture in differentiation medium (DFNB) of an ESC line constitutively expressing Gli1-FLAG transgene from Rosa26 promoter. Two days into the suspension culture, cells were induced with 500nM of all-trans retinoic acid for additional 3 days before harvested for total RNA extraction.
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| Sample_geo_accession | GSM1045179
| | Sample_status | Public on Dec 15 2012
| | Sample_submission_date | Nov 27 2012
| | Sample_last_update_date | Dec 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated for 3 days with all trans retinoic acid (500nM) or all trans retinoic acid (500nM) and Smo agonist (Ag1.3, 50nM).
| | Sample_growth_protocol_ch1 | Embryoid bodies were formed by culturing Rosa26-Gli1-FLAG ESCs in low attachment plates in suspension in DFNK medium. After two days of the suspension culture, cells were treated with differentiation inducers (see below) for 3 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with mirVana kit from Ambion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard protocol (3' IVT express kit, Affymetrix, P/N 901228) from 2.5ug total RNA
| | Sample_hyb_protocol | 13.5 mg of fragmented biotinylated cRNA was fragmented and hybridized for 16 hr at 45C on Mouse Genome 430 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Arrays were scanned with the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with dChip
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kevin,,Peterson
| | Sample_contact_email | kevin.peterson@med.usc.edu
| | Sample_contact_phone | 323-442-8077
| | Sample_contact_fax | 323-442-8024
| | Sample_contact_laboratory | Andrew McMahon
| | Sample_contact_department | Department of Stem Cell Biology and Regenerative Medicine
| | Sample_contact_institute | Eli and Edythe Broad-CIRM Center for Regenerative Medicine, University of Southern California Keck School of Medicine
| | Sample_contact_address | 1425 San Pablo St.
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1045nnn/GSM1045179/suppl/GSM1045179_4-26_RA.CEL.gz
| | Sample_series_id | GSE42565
| | Sample_series_id | GSE42594
| | Sample_data_row_count | 45101
| | |
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GSM1045180 | GPL1261 |
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NEB_RA_rep2
|
Neuralized embryoid bodies, all trans retinoic acid (500nM), 3 days
|
tissue: Gli1-FLAG ESC-derived neural progenitors
treatment: all trans retinoic acid (500nM)
|
Neural progenitors were formed by suspension culture in differentiation medium (DFNB) of an ESC line constitutively expressing Gli1-FLAG transgene from Rosa26 promoter. Two days into the suspension culture, cells were induced with 500nM of all-trans retinoic acid for additional 3 days before harvested for total RNA extraction.
|
| Sample_geo_accession | GSM1045180
| | Sample_status | Public on Dec 15 2012
| | Sample_submission_date | Nov 27 2012
| | Sample_last_update_date | Dec 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated for 3 days with all trans retinoic acid (500nM) or all trans retinoic acid (500nM) and Smo agonist (Ag1.3, 50nM).
| | Sample_growth_protocol_ch1 | Embryoid bodies were formed by culturing Rosa26-Gli1-FLAG ESCs in low attachment plates in suspension in DFNK medium. After two days of the suspension culture, cells were treated with differentiation inducers (see below) for 3 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with mirVana kit from Ambion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard protocol (3' IVT express kit, Affymetrix, P/N 901228) from 2.5ug total RNA
| | Sample_hyb_protocol | 13.5 mg of fragmented biotinylated cRNA was fragmented and hybridized for 16 hr at 45C on Mouse Genome 430 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Arrays were scanned with the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with dChip
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kevin,,Peterson
| | Sample_contact_email | kevin.peterson@med.usc.edu
| | Sample_contact_phone | 323-442-8077
| | Sample_contact_fax | 323-442-8024
| | Sample_contact_laboratory | Andrew McMahon
| | Sample_contact_department | Department of Stem Cell Biology and Regenerative Medicine
| | Sample_contact_institute | Eli and Edythe Broad-CIRM Center for Regenerative Medicine, University of Southern California Keck School of Medicine
| | Sample_contact_address | 1425 San Pablo St.
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1045nnn/GSM1045180/suppl/GSM1045180_4-29_RA.CEL.gz
| | Sample_series_id | GSE42565
| | Sample_series_id | GSE42594
| | Sample_data_row_count | 45101
| | |
|
GSM1045181 | GPL1261 |
|
NEB_RA_rep3
|
Neuralized embryoid bodies, all trans retinoic acid (500nM), 3 days
|
tissue: Gli1-FLAG ESC-derived neural progenitors
treatment: all trans retinoic acid (500nM)
|
Neural progenitors were formed by suspension culture in differentiation medium (DFNB) of an ESC line constitutively expressing Gli1-FLAG transgene from Rosa26 promoter. Two days into the suspension culture, cells were induced with 500nM of all-trans retinoic acid for additional 3 days before harvested for total RNA extraction.
|
| Sample_geo_accession | GSM1045181
| | Sample_status | Public on Dec 15 2012
| | Sample_submission_date | Nov 27 2012
| | Sample_last_update_date | Dec 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated for 3 days with all trans retinoic acid (500nM) or all trans retinoic acid (500nM) and Smo agonist (Ag1.3, 50nM).
| | Sample_growth_protocol_ch1 | Embryoid bodies were formed by culturing Rosa26-Gli1-FLAG ESCs in low attachment plates in suspension in DFNK medium. After two days of the suspension culture, cells were treated with differentiation inducers (see below) for 3 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with mirVana kit from Ambion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard protocol (3' IVT express kit, Affymetrix, P/N 901228) from 2.5ug total RNA
| | Sample_hyb_protocol | 13.5 mg of fragmented biotinylated cRNA was fragmented and hybridized for 16 hr at 45C on Mouse Genome 430 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Arrays were scanned with the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with dChip
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kevin,,Peterson
| | Sample_contact_email | kevin.peterson@med.usc.edu
| | Sample_contact_phone | 323-442-8077
| | Sample_contact_fax | 323-442-8024
| | Sample_contact_laboratory | Andrew McMahon
| | Sample_contact_department | Department of Stem Cell Biology and Regenerative Medicine
| | Sample_contact_institute | Eli and Edythe Broad-CIRM Center for Regenerative Medicine, University of Southern California Keck School of Medicine
| | Sample_contact_address | 1425 San Pablo St.
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1045nnn/GSM1045181/suppl/GSM1045181_5-11_RA.CEL.gz
| | Sample_series_id | GSE42565
| | Sample_series_id | GSE42594
| | Sample_data_row_count | 45101
| | |
|
GSM1045182 | GPL1261 |
|
NEB_RA-Ag1.3_rep1
|
Neuralized embryoid bodies, all trans retinoic acid (500nM) and Smo agonist (Ag1.3), 3 days
|
tissue: Gli1-FLAG ESC-derived neural progenitors
treatment: all trans retinoic acid (500nM) and Smo agonist (Ag1.3, 50nM)
|
Neural progenitors were formed by suspension culture in differentiation medium (DFNB) of an ESC line constitutively expressing Gli1-FLAG transgene from Rosa26 promoter. Two days into the suspension culture, cells were induced with 500nM of all-trans retinoic acid and 50nM of Smo agonist (Ag1.3) for additional 3 days before harvested for total RNA extraction.
|
| Sample_geo_accession | GSM1045182
| | Sample_status | Public on Dec 15 2012
| | Sample_submission_date | Nov 27 2012
| | Sample_last_update_date | Dec 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated for 3 days with all trans retinoic acid (500nM) or all trans retinoic acid (500nM) and Smo agonist (Ag1.3, 50nM).
| | Sample_growth_protocol_ch1 | Embryoid bodies were formed by culturing Rosa26-Gli1-FLAG ESCs in low attachment plates in suspension in DFNK medium. After two days of the suspension culture, cells were treated with differentiation inducers (see below) for 3 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with mirVana kit from Ambion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard protocol (3' IVT express kit, Affymetrix, P/N 901228) from 2.5ug total RNA
| | Sample_hyb_protocol | 13.5 mg of fragmented biotinylated cRNA was fragmented and hybridized for 16 hr at 45C on Mouse Genome 430 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Arrays were scanned with the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with dChip
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kevin,,Peterson
| | Sample_contact_email | kevin.peterson@med.usc.edu
| | Sample_contact_phone | 323-442-8077
| | Sample_contact_fax | 323-442-8024
| | Sample_contact_laboratory | Andrew McMahon
| | Sample_contact_department | Department of Stem Cell Biology and Regenerative Medicine
| | Sample_contact_institute | Eli and Edythe Broad-CIRM Center for Regenerative Medicine, University of Southern California Keck School of Medicine
| | Sample_contact_address | 1425 San Pablo St.
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1045nnn/GSM1045182/suppl/GSM1045182_4-26_Ag.CEL.gz
| | Sample_series_id | GSE42565
| | Sample_series_id | GSE42594
| | Sample_data_row_count | 45101
| | |
|
GSM1045183 | GPL1261 |
|
NEB_RA-Ag1.3_rep2
|
Neuralized embryoid bodies, all trans retinoic acid (500nM) and Smo agonist (Ag1.3), 3 days
|
tissue: Gli1-FLAG ESC-derived neural progenitors
treatment: all trans retinoic acid (500nM) and Smo agonist (Ag1.3, 50nM)
|
Neural progenitors were formed by suspension culture in differentiation medium (DFNB) of an ESC line constitutively expressing Gli1-FLAG transgene from Rosa26 promoter. Two days into the suspension culture, cells were induced with 500nM of all-trans retinoic acid and 50nM of Smo agonist (Ag1.3) for additional 3 days before harvested for total RNA extraction.
|
| Sample_geo_accession | GSM1045183
| | Sample_status | Public on Dec 15 2012
| | Sample_submission_date | Nov 27 2012
| | Sample_last_update_date | Dec 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated for 3 days with all trans retinoic acid (500nM) or all trans retinoic acid (500nM) and Smo agonist (Ag1.3, 50nM).
| | Sample_growth_protocol_ch1 | Embryoid bodies were formed by culturing Rosa26-Gli1-FLAG ESCs in low attachment plates in suspension in DFNK medium. After two days of the suspension culture, cells were treated with differentiation inducers (see below) for 3 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with mirVana kit from Ambion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard protocol (3' IVT express kit, Affymetrix, P/N 901228) from 2.5ug total RNA
| | Sample_hyb_protocol | 13.5 mg of fragmented biotinylated cRNA was fragmented and hybridized for 16 hr at 45C on Mouse Genome 430 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Arrays were scanned with the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with dChip
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kevin,,Peterson
| | Sample_contact_email | kevin.peterson@med.usc.edu
| | Sample_contact_phone | 323-442-8077
| | Sample_contact_fax | 323-442-8024
| | Sample_contact_laboratory | Andrew McMahon
| | Sample_contact_department | Department of Stem Cell Biology and Regenerative Medicine
| | Sample_contact_institute | Eli and Edythe Broad-CIRM Center for Regenerative Medicine, University of Southern California Keck School of Medicine
| | Sample_contact_address | 1425 San Pablo St.
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1045nnn/GSM1045183/suppl/GSM1045183_4-29_Ag.CEL.gz
| | Sample_series_id | GSE42565
| | Sample_series_id | GSE42594
| | Sample_data_row_count | 45101
| | |
|
GSM1045184 | GPL1261 |
|
NEB_RA-Ag1.3_rep3
|
Neuralized embryoid bodies, all trans retinoic acid (500nM) and Smo agonist (Ag1.3), 3 days
|
tissue: Gli1-FLAG ESC-derived neural progenitors
treatment: all trans retinoic acid (500nM) and Smo agonist (Ag1.3, 50nM)
|
Neural progenitors were formed by suspension culture in differentiation medium (DFNB) of an ESC line constitutively expressing Gli1-FLAG transgene from Rosa26 promoter. Two days into the suspension culture, cells were induced with 500nM of all-trans retinoic acid and 50nM of Smo agonist (Ag1.3) for additional 3 days before harvested for total RNA extraction.
|
| Sample_geo_accession | GSM1045184
| | Sample_status | Public on Dec 15 2012
| | Sample_submission_date | Nov 27 2012
| | Sample_last_update_date | Dec 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were treated for 3 days with all trans retinoic acid (500nM) or all trans retinoic acid (500nM) and Smo agonist (Ag1.3, 50nM).
| | Sample_growth_protocol_ch1 | Embryoid bodies were formed by culturing Rosa26-Gli1-FLAG ESCs in low attachment plates in suspension in DFNK medium. After two days of the suspension culture, cells were treated with differentiation inducers (see below) for 3 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with mirVana kit from Ambion
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard protocol (3' IVT express kit, Affymetrix, P/N 901228) from 2.5ug total RNA
| | Sample_hyb_protocol | 13.5 mg of fragmented biotinylated cRNA was fragmented and hybridized for 16 hr at 45C on Mouse Genome 430 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Arrays were scanned with the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with dChip
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Kevin,,Peterson
| | Sample_contact_email | kevin.peterson@med.usc.edu
| | Sample_contact_phone | 323-442-8077
| | Sample_contact_fax | 323-442-8024
| | Sample_contact_laboratory | Andrew McMahon
| | Sample_contact_department | Department of Stem Cell Biology and Regenerative Medicine
| | Sample_contact_institute | Eli and Edythe Broad-CIRM Center for Regenerative Medicine, University of Southern California Keck School of Medicine
| | Sample_contact_address | 1425 San Pablo St.
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1045nnn/GSM1045184/suppl/GSM1045184_5-11_Ag.CEL.gz
| | Sample_series_id | GSE42565
| | Sample_series_id | GSE42594
| | Sample_data_row_count | 45101
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