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Search results for the GEO ID: GSE39422

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GSM967943

GPL1261

Day0_rep1

ES to Motor Neuron differentiation, Day0

cell-line: Ainv15 (ATCC SCRC-1029) with Dox-inducible Cdx2-V5 construct cell-treatment: none time: Day0 cell type: ES cells

ES to Motor Neuron differentiation, Day0

Sample_geo_accession	GSM967943
Sample_status	Public on Jul 04 2013
Sample_submission_date	Jul 17 2012
Sample_last_update_date	Jul 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). 2ug/ml Doxycycline (Sigma) and 100 ng/ml bFGF (PeproTech) were added to the culture medium on Day 3 when required.
Sample_growth_protocol_ch1	ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described. Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x10^5 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). On Day 3, cultures were treated with Doxycycline (Dox) (2 µg/ml) for 6 to 8 hours. Cultures were collected, washed with PBS, and treated with 100 nM RA, 100 ng/ml bFGF (PeproTech), and 100 nM Hh agonist and medium was changed on Day 5. For ChIP experiments, the same conditions were used but scaled to seed 1x10^7 cells on Day 0.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted with Qiagen RNAeasy at different time points following manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was amplified using NuGen Ovation amplification and labeling kit according to manufacturer’s instructions
Sample_hyb_protocol	RNA was hybridized to Affymetrix Mouse Genome 430 2.0 microarrays.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000.
Sample_data_processing	Data analysis was carried out using the affylmGUI BioConductor package. GCRMA normalization was performed across all arrays, followed by linear model fitting using Limma. Differentially expressed genes were defined by ranking all probesets by the moderated t-statistic-derived p-value (adjusted for multiple hypothesis testing using Benjamini & Hochberg’s method and setting thresholds of p<0.001 and a fold-change of at least 2.
Sample_platform_id	GPL1261
Sample_contact_name	Shaun,,Mahony
Sample_contact_email	mahony@psu.edu
Sample_contact_phone	814-865-3008
Sample_contact_laboratory	Shaun Mahony
Sample_contact_department	Biochemistry & Molecular Biology
Sample_contact_institute	Penn State University
Sample_contact_address	450 North Frear Bldg
Sample_contact_city	University Park
Sample_contact_state	PA
Sample_contact_zip/postal_code	16802
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967943/suppl/GSM967943_0_r1.CEL.gz
Sample_series_id	GSE39422
Sample_series_id	GSE39453
Sample_data_row_count	45101

GSM967944

GPL1261

Day0_rep2

ES to Motor Neuron differentiation, Day0

cell-line: Ainv15 (ATCC SCRC-1029) with Dox-inducible Cdx2-V5 construct cell-treatment: none time: Day0 cell type: ES cells

ES to Motor Neuron differentiation, Day0

Sample_geo_accession	GSM967944
Sample_status	Public on Jul 04 2013
Sample_submission_date	Jul 17 2012
Sample_last_update_date	Jul 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). 2ug/ml Doxycycline (Sigma) and 100 ng/ml bFGF (PeproTech) were added to the culture medium on Day 3 when required.
Sample_growth_protocol_ch1	ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described. Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x10^5 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). On Day 3, cultures were treated with Doxycycline (Dox) (2 µg/ml) for 6 to 8 hours. Cultures were collected, washed with PBS, and treated with 100 nM RA, 100 ng/ml bFGF (PeproTech), and 100 nM Hh agonist and medium was changed on Day 5. For ChIP experiments, the same conditions were used but scaled to seed 1x10^7 cells on Day 0.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted with Qiagen RNAeasy at different time points following manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was amplified using NuGen Ovation amplification and labeling kit according to manufacturer’s instructions
Sample_hyb_protocol	RNA was hybridized to Affymetrix Mouse Genome 430 2.0 microarrays.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000.
Sample_data_processing	Data analysis was carried out using the affylmGUI BioConductor package. GCRMA normalization was performed across all arrays, followed by linear model fitting using Limma. Differentially expressed genes were defined by ranking all probesets by the moderated t-statistic-derived p-value (adjusted for multiple hypothesis testing using Benjamini & Hochberg’s method and setting thresholds of p<0.001 and a fold-change of at least 2.
Sample_platform_id	GPL1261
Sample_contact_name	Shaun,,Mahony
Sample_contact_email	mahony@psu.edu
Sample_contact_phone	814-865-3008
Sample_contact_laboratory	Shaun Mahony
Sample_contact_department	Biochemistry & Molecular Biology
Sample_contact_institute	Penn State University
Sample_contact_address	450 North Frear Bldg
Sample_contact_city	University Park
Sample_contact_state	PA
Sample_contact_zip/postal_code	16802
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967944/suppl/GSM967944_0_r2.CEL.gz
Sample_series_id	GSE39422
Sample_series_id	GSE39453
Sample_data_row_count	45101

GSM967945

GPL1261

Day0_rep3

ES to Motor Neuron differentiation, Day0

cell-line: Ainv15 (ATCC SCRC-1029) with Dox-inducible Cdx2-V5 construct cell-treatment: none time: Day0 cell type: ES cells

ES to Motor Neuron differentiation, Day0

Sample_geo_accession	GSM967945
Sample_status	Public on Jul 04 2013
Sample_submission_date	Jul 17 2012
Sample_last_update_date	Jul 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). 2ug/ml Doxycycline (Sigma) and 100 ng/ml bFGF (PeproTech) were added to the culture medium on Day 3 when required.
Sample_growth_protocol_ch1	ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described. Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x10^5 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). On Day 3, cultures were treated with Doxycycline (Dox) (2 µg/ml) for 6 to 8 hours. Cultures were collected, washed with PBS, and treated with 100 nM RA, 100 ng/ml bFGF (PeproTech), and 100 nM Hh agonist and medium was changed on Day 5. For ChIP experiments, the same conditions were used but scaled to seed 1x10^7 cells on Day 0.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted with Qiagen RNAeasy at different time points following manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was amplified using NuGen Ovation amplification and labeling kit according to manufacturer’s instructions
Sample_hyb_protocol	RNA was hybridized to Affymetrix Mouse Genome 430 2.0 microarrays.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000.
Sample_data_processing	Data analysis was carried out using the affylmGUI BioConductor package. GCRMA normalization was performed across all arrays, followed by linear model fitting using Limma. Differentially expressed genes were defined by ranking all probesets by the moderated t-statistic-derived p-value (adjusted for multiple hypothesis testing using Benjamini & Hochberg’s method and setting thresholds of p<0.001 and a fold-change of at least 2.
Sample_platform_id	GPL1261
Sample_contact_name	Shaun,,Mahony
Sample_contact_email	mahony@psu.edu
Sample_contact_phone	814-865-3008
Sample_contact_laboratory	Shaun Mahony
Sample_contact_department	Biochemistry & Molecular Biology
Sample_contact_institute	Penn State University
Sample_contact_address	450 North Frear Bldg
Sample_contact_city	University Park
Sample_contact_state	PA
Sample_contact_zip/postal_code	16802
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967945/suppl/GSM967945_0_r3.CEL.gz
Sample_series_id	GSE39422
Sample_series_id	GSE39453
Sample_data_row_count	45101

GSM967946

GPL1261

Day5_MN_rep1

ES to Motor Neuron differentiation, Day5 motor neurons

cell-line: Ainv15 (ATCC SCRC-1029) with Dox-inducible Cdx2-V5 construct cell-treatment: +RA +Hh time: Day5 cell type: motor neurons

ES to Motor Neuron differentiation, Day5 motor neurons

Sample_geo_accession	GSM967946
Sample_status	Public on Jul 04 2013
Sample_submission_date	Jul 17 2012
Sample_last_update_date	Jul 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). 2ug/ml Doxycycline (Sigma) and 100 ng/ml bFGF (PeproTech) were added to the culture medium on Day 3 when required.
Sample_growth_protocol_ch1	ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described. Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x10^5 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). On Day 3, cultures were treated with Doxycycline (Dox) (2 µg/ml) for 6 to 8 hours. Cultures were collected, washed with PBS, and treated with 100 nM RA, 100 ng/ml bFGF (PeproTech), and 100 nM Hh agonist and medium was changed on Day 5. For ChIP experiments, the same conditions were used but scaled to seed 1x10^7 cells on Day 0.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted with Qiagen RNAeasy at different time points following manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was amplified using NuGen Ovation amplification and labeling kit according to manufacturer’s instructions
Sample_hyb_protocol	RNA was hybridized to Affymetrix Mouse Genome 430 2.0 microarrays.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000.
Sample_data_processing	Data analysis was carried out using the affylmGUI BioConductor package. GCRMA normalization was performed across all arrays, followed by linear model fitting using Limma. Differentially expressed genes were defined by ranking all probesets by the moderated t-statistic-derived p-value (adjusted for multiple hypothesis testing using Benjamini & Hochberg’s method and setting thresholds of p<0.001 and a fold-change of at least 2.
Sample_platform_id	GPL1261
Sample_contact_name	Shaun,,Mahony
Sample_contact_email	mahony@psu.edu
Sample_contact_phone	814-865-3008
Sample_contact_laboratory	Shaun Mahony
Sample_contact_department	Biochemistry & Molecular Biology
Sample_contact_institute	Penn State University
Sample_contact_address	450 North Frear Bldg
Sample_contact_city	University Park
Sample_contact_state	PA
Sample_contact_zip/postal_code	16802
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967946/suppl/GSM967946_iCdx2_RAHh_Day5_1.CEL.gz
Sample_series_id	GSE39422
Sample_series_id	GSE39453
Sample_data_row_count	45101

GSM967947

GPL1261

Day5_MN_rep2

ES to Motor Neuron differentiation, Day5 motor neurons

cell-line: Ainv15 (ATCC SCRC-1029) with Dox-inducible Cdx2-V5 construct cell-treatment: +RA +Hh time: Day5 cell type: motor neurons

ES to Motor Neuron differentiation, Day5 motor neurons

Sample_geo_accession	GSM967947
Sample_status	Public on Jul 04 2013
Sample_submission_date	Jul 17 2012
Sample_last_update_date	Jul 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). 2ug/ml Doxycycline (Sigma) and 100 ng/ml bFGF (PeproTech) were added to the culture medium on Day 3 when required.
Sample_growth_protocol_ch1	ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described. Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x10^5 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). On Day 3, cultures were treated with Doxycycline (Dox) (2 µg/ml) for 6 to 8 hours. Cultures were collected, washed with PBS, and treated with 100 nM RA, 100 ng/ml bFGF (PeproTech), and 100 nM Hh agonist and medium was changed on Day 5. For ChIP experiments, the same conditions were used but scaled to seed 1x10^7 cells on Day 0.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted with Qiagen RNAeasy at different time points following manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was amplified using NuGen Ovation amplification and labeling kit according to manufacturer’s instructions
Sample_hyb_protocol	RNA was hybridized to Affymetrix Mouse Genome 430 2.0 microarrays.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000.
Sample_data_processing	Data analysis was carried out using the affylmGUI BioConductor package. GCRMA normalization was performed across all arrays, followed by linear model fitting using Limma. Differentially expressed genes were defined by ranking all probesets by the moderated t-statistic-derived p-value (adjusted for multiple hypothesis testing using Benjamini & Hochberg’s method and setting thresholds of p<0.001 and a fold-change of at least 2.
Sample_platform_id	GPL1261
Sample_contact_name	Shaun,,Mahony
Sample_contact_email	mahony@psu.edu
Sample_contact_phone	814-865-3008
Sample_contact_laboratory	Shaun Mahony
Sample_contact_department	Biochemistry & Molecular Biology
Sample_contact_institute	Penn State University
Sample_contact_address	450 North Frear Bldg
Sample_contact_city	University Park
Sample_contact_state	PA
Sample_contact_zip/postal_code	16802
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967947/suppl/GSM967947_iCdx2_RAHh_Day5_2.CEL.gz
Sample_series_id	GSE39422
Sample_series_id	GSE39453
Sample_data_row_count	45101

GSM967948

GPL1261

Day5_MN_rep3

ES to Motor Neuron differentiation, Day5 motor neurons

cell-line: Ainv15 (ATCC SCRC-1029) with Dox-inducible Cdx2-V5 construct cell-treatment: +RA +Hh time: Day5 cell type: motor neurons

ES to Motor Neuron differentiation, Day5 motor neurons

Sample_geo_accession	GSM967948
Sample_status	Public on Jul 04 2013
Sample_submission_date	Jul 17 2012
Sample_last_update_date	Jul 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). 2ug/ml Doxycycline (Sigma) and 100 ng/ml bFGF (PeproTech) were added to the culture medium on Day 3 when required.
Sample_growth_protocol_ch1	ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described. Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x10^5 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). On Day 3, cultures were treated with Doxycycline (Dox) (2 µg/ml) for 6 to 8 hours. Cultures were collected, washed with PBS, and treated with 100 nM RA, 100 ng/ml bFGF (PeproTech), and 100 nM Hh agonist and medium was changed on Day 5. For ChIP experiments, the same conditions were used but scaled to seed 1x10^7 cells on Day 0.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted with Qiagen RNAeasy at different time points following manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was amplified using NuGen Ovation amplification and labeling kit according to manufacturer’s instructions
Sample_hyb_protocol	RNA was hybridized to Affymetrix Mouse Genome 430 2.0 microarrays.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000.
Sample_data_processing	Data analysis was carried out using the affylmGUI BioConductor package. GCRMA normalization was performed across all arrays, followed by linear model fitting using Limma. Differentially expressed genes were defined by ranking all probesets by the moderated t-statistic-derived p-value (adjusted for multiple hypothesis testing using Benjamini & Hochberg’s method and setting thresholds of p<0.001 and a fold-change of at least 2.
Sample_platform_id	GPL1261
Sample_contact_name	Shaun,,Mahony
Sample_contact_email	mahony@psu.edu
Sample_contact_phone	814-865-3008
Sample_contact_laboratory	Shaun Mahony
Sample_contact_department	Biochemistry & Molecular Biology
Sample_contact_institute	Penn State University
Sample_contact_address	450 North Frear Bldg
Sample_contact_city	University Park
Sample_contact_state	PA
Sample_contact_zip/postal_code	16802
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967948/suppl/GSM967948_iCdx2_RAHh_Day5_3.CEL.gz
Sample_series_id	GSE39422
Sample_series_id	GSE39453
Sample_data_row_count	45101

GSM967949

GPL1261

Day5_MN+iCdx2+FGF_rep1

ES to Motor Neuron differentiation, Day5 motor neurons caudalized with iCdx2 and FGF

cell-line: Ainv15 (ATCC SCRC-1029) with Dox-inducible Cdx2-V5 construct cell-treatment: +RA +Hh +Dox +FGF time: Day5 cell type: motor neurons caudalized with iCdx2 and FGF

ES to Motor Neuron differentiation, Day5 motor neurons caudalized with iCdx2 and FGF

Sample_geo_accession	GSM967949
Sample_status	Public on Jul 04 2013
Sample_submission_date	Jul 17 2012
Sample_last_update_date	Jul 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). 2ug/ml Doxycycline (Sigma) and 100 ng/ml bFGF (PeproTech) were added to the culture medium on Day 3 when required.
Sample_growth_protocol_ch1	ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described. Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x10^5 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). On Day 3, cultures were treated with Doxycycline (Dox) (2 µg/ml) for 6 to 8 hours. Cultures were collected, washed with PBS, and treated with 100 nM RA, 100 ng/ml bFGF (PeproTech), and 100 nM Hh agonist and medium was changed on Day 5. For ChIP experiments, the same conditions were used but scaled to seed 1x10^7 cells on Day 0.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted with Qiagen RNAeasy at different time points following manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was amplified using NuGen Ovation amplification and labeling kit according to manufacturer’s instructions
Sample_hyb_protocol	RNA was hybridized to Affymetrix Mouse Genome 430 2.0 microarrays.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000.
Sample_data_processing	Data analysis was carried out using the affylmGUI BioConductor package. GCRMA normalization was performed across all arrays, followed by linear model fitting using Limma. Differentially expressed genes were defined by ranking all probesets by the moderated t-statistic-derived p-value (adjusted for multiple hypothesis testing using Benjamini & Hochberg’s method and setting thresholds of p<0.001 and a fold-change of at least 2.
Sample_platform_id	GPL1261
Sample_contact_name	Shaun,,Mahony
Sample_contact_email	mahony@psu.edu
Sample_contact_phone	814-865-3008
Sample_contact_laboratory	Shaun Mahony
Sample_contact_department	Biochemistry & Molecular Biology
Sample_contact_institute	Penn State University
Sample_contact_address	450 North Frear Bldg
Sample_contact_city	University Park
Sample_contact_state	PA
Sample_contact_zip/postal_code	16802
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967949/suppl/GSM967949_iCdx2_RAHhDoxFGF_Day5_1.CEL.gz
Sample_series_id	GSE39422
Sample_series_id	GSE39453
Sample_data_row_count	45101

GSM967950

GPL1261

Day5_MN+iCdx2+FGF_rep2

ES to Motor Neuron differentiation, Day5 motor neurons caudalized with iCdx2 and FGF

cell-line: Ainv15 (ATCC SCRC-1029) with Dox-inducible Cdx2-V5 construct cell-treatment: +RA +Hh +Dox +FGF time: Day5 cell type: motor neurons caudalized with iCdx2 and FGF

ES to Motor Neuron differentiation, Day5 motor neurons caudalized with iCdx2 and FGF

Sample_geo_accession	GSM967950
Sample_status	Public on Jul 04 2013
Sample_submission_date	Jul 17 2012
Sample_last_update_date	Jul 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). 2ug/ml Doxycycline (Sigma) and 100 ng/ml bFGF (PeproTech) were added to the culture medium on Day 3 when required.
Sample_growth_protocol_ch1	ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described. Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x10^5 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). On Day 3, cultures were treated with Doxycycline (Dox) (2 µg/ml) for 6 to 8 hours. Cultures were collected, washed with PBS, and treated with 100 nM RA, 100 ng/ml bFGF (PeproTech), and 100 nM Hh agonist and medium was changed on Day 5. For ChIP experiments, the same conditions were used but scaled to seed 1x10^7 cells on Day 0.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted with Qiagen RNAeasy at different time points following manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was amplified using NuGen Ovation amplification and labeling kit according to manufacturer’s instructions
Sample_hyb_protocol	RNA was hybridized to Affymetrix Mouse Genome 430 2.0 microarrays.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000.
Sample_data_processing	Data analysis was carried out using the affylmGUI BioConductor package. GCRMA normalization was performed across all arrays, followed by linear model fitting using Limma. Differentially expressed genes were defined by ranking all probesets by the moderated t-statistic-derived p-value (adjusted for multiple hypothesis testing using Benjamini & Hochberg’s method and setting thresholds of p<0.001 and a fold-change of at least 2.
Sample_platform_id	GPL1261
Sample_contact_name	Shaun,,Mahony
Sample_contact_email	mahony@psu.edu
Sample_contact_phone	814-865-3008
Sample_contact_laboratory	Shaun Mahony
Sample_contact_department	Biochemistry & Molecular Biology
Sample_contact_institute	Penn State University
Sample_contact_address	450 North Frear Bldg
Sample_contact_city	University Park
Sample_contact_state	PA
Sample_contact_zip/postal_code	16802
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967950/suppl/GSM967950_iCdx2_RAHhDoxFGF_Day5_2.CEL.gz
Sample_series_id	GSE39422
Sample_series_id	GSE39453
Sample_data_row_count	45101

GSM967951

GPL1261

Day5_MN+iCdx2+FGF_rep3

ES to Motor Neuron differentiation, Day5 motor neurons caudalized with iCdx2 and FGF

cell-line: Ainv15 (ATCC SCRC-1029) with Dox-inducible Cdx2-V5 construct cell-treatment: +RA +Hh +Dox +FGF time: Day5 cell type: motor neurons caudalized with iCdx2 and FGF

ES to Motor Neuron differentiation, Day5 motor neurons caudalized with iCdx2 and FGF

Sample_geo_accession	GSM967951
Sample_status	Public on Jul 04 2013
Sample_submission_date	Jul 17 2012
Sample_last_update_date	Jul 04 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). 2ug/ml Doxycycline (Sigma) and 100 ng/ml bFGF (PeproTech) were added to the culture medium on Day 3 when required.
Sample_growth_protocol_ch1	ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described. Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x10^5 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). On Day 3, cultures were treated with Doxycycline (Dox) (2 µg/ml) for 6 to 8 hours. Cultures were collected, washed with PBS, and treated with 100 nM RA, 100 ng/ml bFGF (PeproTech), and 100 nM Hh agonist and medium was changed on Day 5. For ChIP experiments, the same conditions were used but scaled to seed 1x10^7 cells on Day 0.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted with Qiagen RNAeasy at different time points following manufacturer’s instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was amplified using NuGen Ovation amplification and labeling kit according to manufacturer’s instructions
Sample_hyb_protocol	RNA was hybridized to Affymetrix Mouse Genome 430 2.0 microarrays.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000.
Sample_data_processing	Data analysis was carried out using the affylmGUI BioConductor package. GCRMA normalization was performed across all arrays, followed by linear model fitting using Limma. Differentially expressed genes were defined by ranking all probesets by the moderated t-statistic-derived p-value (adjusted for multiple hypothesis testing using Benjamini & Hochberg’s method and setting thresholds of p<0.001 and a fold-change of at least 2.
Sample_platform_id	GPL1261
Sample_contact_name	Shaun,,Mahony
Sample_contact_email	mahony@psu.edu
Sample_contact_phone	814-865-3008
Sample_contact_laboratory	Shaun Mahony
Sample_contact_department	Biochemistry & Molecular Biology
Sample_contact_institute	Penn State University
Sample_contact_address	450 North Frear Bldg
Sample_contact_city	University Park
Sample_contact_state	PA
Sample_contact_zip/postal_code	16802
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967951/suppl/GSM967951_iCdx2_RAHhDoxFGF_Day5_3.CEL.gz
Sample_series_id	GSE39422
Sample_series_id	GSE39453
Sample_data_row_count	45101

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