Search results for the GEO ID: GSE40751  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1000612 | GPL570 |
|
Migratory hiPSCs-NSCs towards U87, biological rep1
|
hiPSCs-NSCs migrating towards U87
|
cell type: human induced pluripotent stem cell-derived neural stem cells
|
Gene expression data from migratory hiPSCs derived NSCs towards U87
|
| Sample_geo_accession | GSM1000612
| | Sample_status | Public on Feb 28 2013
| | Sample_submission_date | Sep 10 2012
| | Sample_last_update_date | Feb 28 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Six-well Boyden chambers with 8 μm pore size were utilized for cell separation. hiPSCs-NSCs were seeded at 1 x 106 cells per insert into the upper chamber in 2 ml of Opti-MEM, and the bottom receiver wells were filled with 3 ml of U87 cell-conditioned medium as attractants. A total of 24 chambers were seeded for one tumor type. After incubation at 37°C in 5% CO2 for 16 hours, migratory cells on the bottom of the insert membrane and non-migratory cells on the upper side of the membrane were digested by Accutase and collected. Cells collected from 8 wells were combined into one sample.
| | Sample_growth_protocol_ch1 | hiPSCs derived NSCs were cultured on 0.1 Gelatin coated 6 well plates in NSC medium consisting of DMEM/F12, 2% B27, 2 mM L-glutamine, 20 ng/ml human epidermal growth factor (EGF) , 20 ng/ml bFGF (PeproTech) and penicillin/streptomycin. These cells were split every 3 - 4 days by digested with Accutase and plated at a density of 50,000 to 60,000 cells per cm2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a Trizol method (TRIzol® RNeasy Total RNA Purification Kit, Invitrogen) according to the manufacturer’s instructions. Extracted RNA samples were re-suspended in RNase-free water and then treated with RNase-free DNase (QIAGEN) and RNeasy column purification (QIAGEN)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One microgram of isolated total RNAs from each sample was reverse-transcribed, T7-amplified, fragmented and labelled using Kreatech’s RNA ampULSe amplification and labelling kit according to the instruction manual provided (Kreatech Biotechnology, Amsterdam, Netherlands).
| | Sample_hyb_protocol | Fifteen microgram of the fragmented/labelled cRNA was then hybridised to GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Hybridization was performed for 16 hours in accordance with the user manual provided, followed by washing in GeneChip® Fluidics Station 450 (Affymetrix)
| | Sample_scan_protocol | GeneChips were scanned on a GeneChip® Scanner 3000 (Affymetrix) according to the protocol from Affymetrix. GeneChip Command Console Software (AGCC) was used to capture microarray images and quantify signal intensity from each feature.
| | Sample_data_processing | Microarray raw data was acquired using the GCOS software (Affymetrix). Data obtained from GCOS was transferred to GeneSpring GX software (Agilent Technologies, Santa Clara, CA). The data was normalized using the default setting of Genespring. To analyze the data, the genes were grouped according to migratory or non-migratory NSCs towards different tumor attractants. The data was filtered according to their flags in such a way that 3 out of 3 sample replicates fulfilled the conditions of a cut-off of ≥ two-fold difference in expression level and a p-value of less than 0.05. Volcano plot was used to filter the data further.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Can,,Chen
| | Sample_contact_email | a0068186@nus.edu.sg
| | Sample_contact_laboratory | Wang Shu Lab
| | Sample_contact_department | Department of Biological Sciences
| | Sample_contact_institute | National University of Singapore
| | Sample_contact_address | Science Drive 4
| | Sample_contact_city | Singapore
| | Sample_contact_zip/postal_code | 117543
| | Sample_contact_country | Singapore
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000612/suppl/GSM1000612_Migratory_hiPCs-NSCs_U87_BiolRep1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000612/suppl/GSM1000612_Migratory_hiPCs-NSCs_U87_BiolRep1.CHP.gz
| | Sample_series_id | GSE40749
| | Sample_series_id | GSE40751
| | Sample_data_row_count | 54675
| | |
|
GSM1000613 | GPL570 |
|
Migratory hiPSCs-NSCs towards U87, biological rep2
|
hiPSCs-NSCs migrating towards U87
|
cell type: human induced pluripotent stem cell-derived neural stem cells
|
Gene expression data from migratory hiPSCs derived NSCs towards U87
|
| Sample_geo_accession | GSM1000613
| | Sample_status | Public on Feb 28 2013
| | Sample_submission_date | Sep 10 2012
| | Sample_last_update_date | Feb 28 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Six-well Boyden chambers with 8 μm pore size were utilized for cell separation. hiPSCs-NSCs were seeded at 1 x 106 cells per insert into the upper chamber in 2 ml of Opti-MEM, and the bottom receiver wells were filled with 3 ml of U87 cell-conditioned medium as attractants. A total of 24 chambers were seeded for one tumor type. After incubation at 37°C in 5% CO2 for 16 hours, migratory cells on the bottom of the insert membrane and non-migratory cells on the upper side of the membrane were digested by Accutase and collected. Cells collected from 8 wells were combined into one sample.
| | Sample_growth_protocol_ch1 | hiPSCs derived NSCs were cultured on 0.1 Gelatin coated 6 well plates in NSC medium consisting of DMEM/F12, 2% B27, 2 mM L-glutamine, 20 ng/ml human epidermal growth factor (EGF) , 20 ng/ml bFGF (PeproTech) and penicillin/streptomycin. These cells were split every 3 - 4 days by digested with Accutase and plated at a density of 50,000 to 60,000 cells per cm2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a Trizol method (TRIzol® RNeasy Total RNA Purification Kit, Invitrogen) according to the manufacturer’s instructions. Extracted RNA samples were re-suspended in RNase-free water and then treated with RNase-free DNase (QIAGEN) and RNeasy column purification (QIAGEN)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One microgram of isolated total RNAs from each sample was reverse-transcribed, T7-amplified, fragmented and labelled using Kreatech’s RNA ampULSe amplification and labelling kit according to the instruction manual provided (Kreatech Biotechnology, Amsterdam, Netherlands).
| | Sample_hyb_protocol | Fifteen microgram of the fragmented/labelled cRNA was then hybridised to GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Hybridization was performed for 16 hours in accordance with the user manual provided, followed by washing in GeneChip® Fluidics Station 450 (Affymetrix)
| | Sample_scan_protocol | GeneChips were scanned on a GeneChip® Scanner 3000 (Affymetrix) according to the protocol from Affymetrix. GeneChip Command Console Software (AGCC) was used to capture microarray images and quantify signal intensity from each feature.
| | Sample_data_processing | Microarray raw data was acquired using the GCOS software (Affymetrix). Data obtained from GCOS was transferred to GeneSpring GX software (Agilent Technologies, Santa Clara, CA). The data was normalized using the default setting of Genespring. To analyze the data, the genes were grouped according to migratory or non-migratory NSCs towards different tumor attractants. The data was filtered according to their flags in such a way that 3 out of 3 sample replicates fulfilled the conditions of a cut-off of ≥ two-fold difference in expression level and a p-value of less than 0.05. Volcano plot was used to filter the data further.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Can,,Chen
| | Sample_contact_email | a0068186@nus.edu.sg
| | Sample_contact_laboratory | Wang Shu Lab
| | Sample_contact_department | Department of Biological Sciences
| | Sample_contact_institute | National University of Singapore
| | Sample_contact_address | Science Drive 4
| | Sample_contact_city | Singapore
| | Sample_contact_zip/postal_code | 117543
| | Sample_contact_country | Singapore
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000613/suppl/GSM1000613_Migratory_hiPCs-NSCs_U87_BiolRep2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000613/suppl/GSM1000613_Migratory_hiPCs-NSCs_U87_BiolRep2.CHP.gz
| | Sample_series_id | GSE40749
| | Sample_series_id | GSE40751
| | Sample_data_row_count | 54675
| | |
|
GSM1000614 | GPL570 |
|
Migratory hiPSCs-NSCs towards U87, biological rep3
|
hiPSCs-NSCs migrating towards U87
|
cell type: human induced pluripotent stem cell-derived neural stem cells
|
Gene expression data from migratory hiPSCs derived NSCs towards U87
|
| Sample_geo_accession | GSM1000614
| | Sample_status | Public on Feb 28 2013
| | Sample_submission_date | Sep 10 2012
| | Sample_last_update_date | Feb 28 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Six-well Boyden chambers with 8 μm pore size were utilized for cell separation. hiPSCs-NSCs were seeded at 1 x 106 cells per insert into the upper chamber in 2 ml of Opti-MEM, and the bottom receiver wells were filled with 3 ml of U87 cell-conditioned medium as attractants. A total of 24 chambers were seeded for one tumor type. After incubation at 37°C in 5% CO2 for 16 hours, migratory cells on the bottom of the insert membrane and non-migratory cells on the upper side of the membrane were digested by Accutase and collected. Cells collected from 8 wells were combined into one sample.
| | Sample_growth_protocol_ch1 | hiPSCs derived NSCs were cultured on 0.1 Gelatin coated 6 well plates in NSC medium consisting of DMEM/F12, 2% B27, 2 mM L-glutamine, 20 ng/ml human epidermal growth factor (EGF) , 20 ng/ml bFGF (PeproTech) and penicillin/streptomycin. These cells were split every 3 - 4 days by digested with Accutase and plated at a density of 50,000 to 60,000 cells per cm2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a Trizol method (TRIzol® RNeasy Total RNA Purification Kit, Invitrogen) according to the manufacturer’s instructions. Extracted RNA samples were re-suspended in RNase-free water and then treated with RNase-free DNase (QIAGEN) and RNeasy column purification (QIAGEN)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One microgram of isolated total RNAs from each sample was reverse-transcribed, T7-amplified, fragmented and labelled using Kreatech’s RNA ampULSe amplification and labelling kit according to the instruction manual provided (Kreatech Biotechnology, Amsterdam, Netherlands).
| | Sample_hyb_protocol | Fifteen microgram of the fragmented/labelled cRNA was then hybridised to GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Hybridization was performed for 16 hours in accordance with the user manual provided, followed by washing in GeneChip® Fluidics Station 450 (Affymetrix)
| | Sample_scan_protocol | GeneChips were scanned on a GeneChip® Scanner 3000 (Affymetrix) according to the protocol from Affymetrix. GeneChip Command Console Software (AGCC) was used to capture microarray images and quantify signal intensity from each feature.
| | Sample_data_processing | Microarray raw data was acquired using the GCOS software (Affymetrix). Data obtained from GCOS was transferred to GeneSpring GX software (Agilent Technologies, Santa Clara, CA). The data was normalized using the default setting of Genespring. To analyze the data, the genes were grouped according to migratory or non-migratory NSCs towards different tumor attractants. The data was filtered according to their flags in such a way that 3 out of 3 sample replicates fulfilled the conditions of a cut-off of ≥ two-fold difference in expression level and a p-value of less than 0.05. Volcano plot was used to filter the data further.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Can,,Chen
| | Sample_contact_email | a0068186@nus.edu.sg
| | Sample_contact_laboratory | Wang Shu Lab
| | Sample_contact_department | Department of Biological Sciences
| | Sample_contact_institute | National University of Singapore
| | Sample_contact_address | Science Drive 4
| | Sample_contact_city | Singapore
| | Sample_contact_zip/postal_code | 117543
| | Sample_contact_country | Singapore
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000614/suppl/GSM1000614_Migratory_hiPCs-NSCs_U87_BiolRep3.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000614/suppl/GSM1000614_Migratory_hiPCs-NSCs_U87_BiolRep3.CHP.gz
| | Sample_series_id | GSE40749
| | Sample_series_id | GSE40751
| | Sample_data_row_count | 54675
| | |
|
GSM1000615 | GPL570 |
|
Non-migratory hiPSCs-NSCs towards U87, biological rep1
|
hiPSCs-NSCs not migrating towards U87
|
cell type: human induced pluripotent stem cell-derived neural stem cells
|
Gene expression data from non-migratory hiPSCs derived NSCs towards U87
|
| Sample_geo_accession | GSM1000615
| | Sample_status | Public on Feb 28 2013
| | Sample_submission_date | Sep 10 2012
| | Sample_last_update_date | Feb 28 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Six-well Boyden chambers with 8 μm pore size were utilized for cell separation. hiPSCs-NSCs were seeded at 1 x 106 cells per insert into the upper chamber in 2 ml of Opti-MEM, and the bottom receiver wells were filled with 3 ml of U87 cell-conditioned medium as attractants. A total of 24 chambers were seeded for one tumor type. After incubation at 37°C in 5% CO2 for 16 hours, migratory cells on the bottom of the insert membrane and non-migratory cells on the upper side of the membrane were digested by Accutase and collected. Cells collected from 8 wells were combined into one sample.
| | Sample_growth_protocol_ch1 | hiPSCs derived NSCs were cultured on 0.1 Gelatin coated 6 well plates in NSC medium consisting of DMEM/F12, 2% B27, 2 mM L-glutamine, 20 ng/ml human epidermal growth factor (EGF) , 20 ng/ml bFGF (PeproTech) and penicillin/streptomycin. These cells were split every 3 - 4 days by digested with Accutase and plated at a density of 50,000 to 60,000 cells per cm2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a Trizol method (TRIzol® RNeasy Total RNA Purification Kit, Invitrogen) according to the manufacturer’s instructions. Extracted RNA samples were re-suspended in RNase-free water and then treated with RNase-free DNase (QIAGEN) and RNeasy column purification (QIAGEN)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One microgram of isolated total RNAs from each sample was reverse-transcribed, T7-amplified, fragmented and labelled using Kreatech’s RNA ampULSe amplification and labelling kit according to the instruction manual provided (Kreatech Biotechnology, Amsterdam, Netherlands).
| | Sample_hyb_protocol | Fifteen microgram of the fragmented/labelled cRNA was then hybridised to GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Hybridization was performed for 16 hours in accordance with the user manual provided, followed by washing in GeneChip® Fluidics Station 450 (Affymetrix)
| | Sample_scan_protocol | GeneChips were scanned on a GeneChip® Scanner 3000 (Affymetrix) according to the protocol from Affymetrix. GeneChip Command Console Software (AGCC) was used to capture microarray images and quantify signal intensity from each feature.
| | Sample_data_processing | Microarray raw data was acquired using the GCOS software (Affymetrix). Data obtained from GCOS was transferred to GeneSpring GX software (Agilent Technologies, Santa Clara, CA). The data was normalized using the default setting of Genespring. To analyze the data, the genes were grouped according to migratory or non-migratory NSCs towards different tumor attractants. The data was filtered according to their flags in such a way that 3 out of 3 sample replicates fulfilled the conditions of a cut-off of ≥ two-fold difference in expression level and a p-value of less than 0.05. Volcano plot was used to filter the data further.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Can,,Chen
| | Sample_contact_email | a0068186@nus.edu.sg
| | Sample_contact_laboratory | Wang Shu Lab
| | Sample_contact_department | Department of Biological Sciences
| | Sample_contact_institute | National University of Singapore
| | Sample_contact_address | Science Drive 4
| | Sample_contact_city | Singapore
| | Sample_contact_zip/postal_code | 117543
| | Sample_contact_country | Singapore
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000615/suppl/GSM1000615_Non-migratory_hiPCs-NSCs_U87_BiolRep1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000615/suppl/GSM1000615_Non-migratory_hiPCs-NSCs_U87_BiolRep1.CHP.gz
| | Sample_series_id | GSE40749
| | Sample_series_id | GSE40751
| | Sample_data_row_count | 54675
| | |
|
GSM1000616 | GPL570 |
|
Non-migratory hiPSCs-NSCs towards U87, biological rep2
|
hiPSCs-NSCs not migrating towards U87
|
cell type: human induced pluripotent stem cell-derived neural stem cells
|
Gene expression data from non-migratory hiPSCs derived NSCs towards U87
|
| Sample_geo_accession | GSM1000616
| | Sample_status | Public on Feb 28 2013
| | Sample_submission_date | Sep 10 2012
| | Sample_last_update_date | Feb 28 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Six-well Boyden chambers with 8 μm pore size were utilized for cell separation. hiPSCs-NSCs were seeded at 1 x 106 cells per insert into the upper chamber in 2 ml of Opti-MEM, and the bottom receiver wells were filled with 3 ml of U87 cell-conditioned medium as attractants. A total of 24 chambers were seeded for one tumor type. After incubation at 37°C in 5% CO2 for 16 hours, migratory cells on the bottom of the insert membrane and non-migratory cells on the upper side of the membrane were digested by Accutase and collected. Cells collected from 8 wells were combined into one sample.
| | Sample_growth_protocol_ch1 | hiPSCs derived NSCs were cultured on 0.1 Gelatin coated 6 well plates in NSC medium consisting of DMEM/F12, 2% B27, 2 mM L-glutamine, 20 ng/ml human epidermal growth factor (EGF) , 20 ng/ml bFGF (PeproTech) and penicillin/streptomycin. These cells were split every 3 - 4 days by digested with Accutase and plated at a density of 50,000 to 60,000 cells per cm2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a Trizol method (TRIzol® RNeasy Total RNA Purification Kit, Invitrogen) according to the manufacturer’s instructions. Extracted RNA samples were re-suspended in RNase-free water and then treated with RNase-free DNase (QIAGEN) and RNeasy column purification (QIAGEN)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One microgram of isolated total RNAs from each sample was reverse-transcribed, T7-amplified, fragmented and labelled using Kreatech’s RNA ampULSe amplification and labelling kit according to the instruction manual provided (Kreatech Biotechnology, Amsterdam, Netherlands).
| | Sample_hyb_protocol | Fifteen microgram of the fragmented/labelled cRNA was then hybridised to GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Hybridization was performed for 16 hours in accordance with the user manual provided, followed by washing in GeneChip® Fluidics Station 450 (Affymetrix)
| | Sample_scan_protocol | GeneChips were scanned on a GeneChip® Scanner 3000 (Affymetrix) according to the protocol from Affymetrix. GeneChip Command Console Software (AGCC) was used to capture microarray images and quantify signal intensity from each feature.
| | Sample_data_processing | Microarray raw data was acquired using the GCOS software (Affymetrix). Data obtained from GCOS was transferred to GeneSpring GX software (Agilent Technologies, Santa Clara, CA). The data was normalized using the default setting of Genespring. To analyze the data, the genes were grouped according to migratory or non-migratory NSCs towards different tumor attractants. The data was filtered according to their flags in such a way that 3 out of 3 sample replicates fulfilled the conditions of a cut-off of ≥ two-fold difference in expression level and a p-value of less than 0.05. Volcano plot was used to filter the data further.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Can,,Chen
| | Sample_contact_email | a0068186@nus.edu.sg
| | Sample_contact_laboratory | Wang Shu Lab
| | Sample_contact_department | Department of Biological Sciences
| | Sample_contact_institute | National University of Singapore
| | Sample_contact_address | Science Drive 4
| | Sample_contact_city | Singapore
| | Sample_contact_zip/postal_code | 117543
| | Sample_contact_country | Singapore
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000616/suppl/GSM1000616_Non-migratory_hiPCs-NSCs_U87_BiolRep2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000616/suppl/GSM1000616_Non-migratory_hiPCs-NSCs_U87_BiolRep2.CHP.gz
| | Sample_series_id | GSE40749
| | Sample_series_id | GSE40751
| | Sample_data_row_count | 54675
| | |
|
GSM1000617 | GPL570 |
|
Non-migratory hiPSCs-NSCs towards U87, biological rep3
|
hiPSCs-NSCs not migrating towards U87
|
cell type: human induced pluripotent stem cell-derived neural stem cells
|
Gene expression data from non-migratory hiPSCs derived NSCs towards U87
|
| Sample_geo_accession | GSM1000617
| | Sample_status | Public on Feb 28 2013
| | Sample_submission_date | Sep 10 2012
| | Sample_last_update_date | Feb 28 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Six-well Boyden chambers with 8 μm pore size were utilized for cell separation. hiPSCs-NSCs were seeded at 1 x 106 cells per insert into the upper chamber in 2 ml of Opti-MEM, and the bottom receiver wells were filled with 3 ml of U87 cell-conditioned medium as attractants. A total of 24 chambers were seeded for one tumor type. After incubation at 37°C in 5% CO2 for 16 hours, migratory cells on the bottom of the insert membrane and non-migratory cells on the upper side of the membrane were digested by Accutase and collected. Cells collected from 8 wells were combined into one sample.
| | Sample_growth_protocol_ch1 | hiPSCs derived NSCs were cultured on 0.1 Gelatin coated 6 well plates in NSC medium consisting of DMEM/F12, 2% B27, 2 mM L-glutamine, 20 ng/ml human epidermal growth factor (EGF) , 20 ng/ml bFGF (PeproTech) and penicillin/streptomycin. These cells were split every 3 - 4 days by digested with Accutase and plated at a density of 50,000 to 60,000 cells per cm2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a Trizol method (TRIzol® RNeasy Total RNA Purification Kit, Invitrogen) according to the manufacturer’s instructions. Extracted RNA samples were re-suspended in RNase-free water and then treated with RNase-free DNase (QIAGEN) and RNeasy column purification (QIAGEN)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One microgram of isolated total RNAs from each sample was reverse-transcribed, T7-amplified, fragmented and labelled using Kreatech’s RNA ampULSe amplification and labelling kit according to the instruction manual provided (Kreatech Biotechnology, Amsterdam, Netherlands).
| | Sample_hyb_protocol | Fifteen microgram of the fragmented/labelled cRNA was then hybridised to GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Hybridization was performed for 16 hours in accordance with the user manual provided, followed by washing in GeneChip® Fluidics Station 450 (Affymetrix)
| | Sample_scan_protocol | GeneChips were scanned on a GeneChip® Scanner 3000 (Affymetrix) according to the protocol from Affymetrix. GeneChip Command Console Software (AGCC) was used to capture microarray images and quantify signal intensity from each feature.
| | Sample_data_processing | Microarray raw data was acquired using the GCOS software (Affymetrix). Data obtained from GCOS was transferred to GeneSpring GX software (Agilent Technologies, Santa Clara, CA). The data was normalized using the default setting of Genespring. To analyze the data, the genes were grouped according to migratory or non-migratory NSCs towards different tumor attractants. The data was filtered according to their flags in such a way that 3 out of 3 sample replicates fulfilled the conditions of a cut-off of ≥ two-fold difference in expression level and a p-value of less than 0.05. Volcano plot was used to filter the data further.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Can,,Chen
| | Sample_contact_email | a0068186@nus.edu.sg
| | Sample_contact_laboratory | Wang Shu Lab
| | Sample_contact_department | Department of Biological Sciences
| | Sample_contact_institute | National University of Singapore
| | Sample_contact_address | Science Drive 4
| | Sample_contact_city | Singapore
| | Sample_contact_zip/postal_code | 117543
| | Sample_contact_country | Singapore
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000617/suppl/GSM1000617_Non-migratory_hiPCs-NSCs_U87_BiolRep3.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000617/suppl/GSM1000617_Non-migratory_hiPCs-NSCs_U87_BiolRep3.CHP.gz
| | Sample_series_id | GSE40749
| | Sample_series_id | GSE40751
| | Sample_data_row_count | 54675
| | |
|
GSM1000618 | GPL570 |
|
Migratory hiPSCs-NSCs towards 4T1, biological rep1
|
hiPSCs-NSCs migrating towards 4T1
|
cell type: human induced pluripotent stem cell-derived neural stem cells
|
Gene expression data from migratory hiPSCs derived NSCs towards 4T1
|
| Sample_geo_accession | GSM1000618
| | Sample_status | Public on Feb 28 2013
| | Sample_submission_date | Sep 10 2012
| | Sample_last_update_date | Feb 28 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Six-well Boyden chambers with 8 μm pore size were utilized for cell separation. hiPSCs-NSCs were seeded at 1 x 106 cells per insert into the upper chamber in 2 ml of Opti-MEM, and the bottom receiver wells were filled with 3 ml of 4T1 cell-conditioned medium as attractants. A total of 24 chambers were seeded for one tumor type. After incubation at 37°C in 5% CO2 for 16 hours, migratory cells on the bottom of the insert membrane and non-migratory cells on the upper side of the membrane were digested by Accutase and collected. Cells collected from 8 wells were combined into one sample.
| | Sample_growth_protocol_ch1 | hiPSCs derived NSCs were cultured on 0.1 Gelatin coated 6 well plates in NSC medium consisting of DMEM/F12, 2% B27, 2 mM L-glutamine, 20 ng/ml human epidermal growth factor (EGF) , 20 ng/ml bFGF (PeproTech) and penicillin/streptomycin. These cells were split every 3 - 4 days by digested with Accutase and plated at a density of 50,000 to 60,000 cells per cm2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a Trizol method (TRIzol® RNeasy Total RNA Purification Kit, Invitrogen) according to the manufacturer’s instructions. Extracted RNA samples were re-suspended in RNase-free water and then treated with RNase-free DNase (QIAGEN) and RNeasy column purification (QIAGEN)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One microgram of isolated total RNAs from each sample was reverse-transcribed, T7-amplified, fragmented and labelled using Kreatech’s RNA ampULSe amplification and labelling kit according to the instruction manual provided (Kreatech Biotechnology, Amsterdam, Netherlands).
| | Sample_hyb_protocol | Fifteen microgram of the fragmented/labelled cRNA was then hybridised to GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Hybridization was performed for 16 hours in accordance with the user manual provided, followed by washing in GeneChip® Fluidics Station 450 (Affymetrix)
| | Sample_scan_protocol | GeneChips were scanned on a GeneChip® Scanner 3000 (Affymetrix) according to the protocol from Affymetrix. GeneChip Command Console Software (AGCC) was used to capture microarray images and quantify signal intensity from each feature.
| | Sample_data_processing | Microarray raw data was acquired using the GCOS software (Affymetrix). Data obtained from GCOS was transferred to GeneSpring GX software (Agilent Technologies, Santa Clara, CA). The data was normalized using the default setting of Genespring. To analyze the data, the genes were grouped according to migratory or non-migratory NSCs towards different tumor attractants. The data was filtered according to their flags in such a way that 3 out of 3 sample replicates fulfilled the conditions of a cut-off of ≥ two-fold difference in expression level and a p-value of less than 0.05. Volcano plot was used to filter the data further.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Can,,Chen
| | Sample_contact_email | a0068186@nus.edu.sg
| | Sample_contact_laboratory | Wang Shu Lab
| | Sample_contact_department | Department of Biological Sciences
| | Sample_contact_institute | National University of Singapore
| | Sample_contact_address | Science Drive 4
| | Sample_contact_city | Singapore
| | Sample_contact_zip/postal_code | 117543
| | Sample_contact_country | Singapore
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000618/suppl/GSM1000618_Migratory_hiPSCs-NSCs_4T1_BiolRep1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000618/suppl/GSM1000618_Migratory_hiPSCs-NSCs_4T1_BiolRep1.CHP.gz
| | Sample_series_id | GSE40750
| | Sample_series_id | GSE40751
| | Sample_data_row_count | 54675
| | |
|
GSM1000619 | GPL570 |
|
Migratory hiPSCs-NSCs towards 4T1, biological rep2
|
hiPSCs-NSCs migrating towards 4T1
|
cell type: human induced pluripotent stem cell-derived neural stem cells
|
Gene expression data from migratory hiPSCs derived NSCs towards 4T1
|
| Sample_geo_accession | GSM1000619
| | Sample_status | Public on Feb 28 2013
| | Sample_submission_date | Sep 10 2012
| | Sample_last_update_date | Feb 28 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Six-well Boyden chambers with 8 μm pore size were utilized for cell separation. hiPSCs-NSCs were seeded at 1 x 106 cells per insert into the upper chamber in 2 ml of Opti-MEM, and the bottom receiver wells were filled with 3 ml of 4T1 cell-conditioned medium as attractants. A total of 24 chambers were seeded for one tumor type. After incubation at 37°C in 5% CO2 for 16 hours, migratory cells on the bottom of the insert membrane and non-migratory cells on the upper side of the membrane were digested by Accutase and collected. Cells collected from 8 wells were combined into one sample.
| | Sample_growth_protocol_ch1 | hiPSCs derived NSCs were cultured on 0.1 Gelatin coated 6 well plates in NSC medium consisting of DMEM/F12, 2% B27, 2 mM L-glutamine, 20 ng/ml human epidermal growth factor (EGF) , 20 ng/ml bFGF (PeproTech) and penicillin/streptomycin. These cells were split every 3 - 4 days by digested with Accutase and plated at a density of 50,000 to 60,000 cells per cm2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a Trizol method (TRIzol® RNeasy Total RNA Purification Kit, Invitrogen) according to the manufacturer’s instructions. Extracted RNA samples were re-suspended in RNase-free water and then treated with RNase-free DNase (QIAGEN) and RNeasy column purification (QIAGEN)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One microgram of isolated total RNAs from each sample was reverse-transcribed, T7-amplified, fragmented and labelled using Kreatech’s RNA ampULSe amplification and labelling kit according to the instruction manual provided (Kreatech Biotechnology, Amsterdam, Netherlands).
| | Sample_hyb_protocol | Fifteen microgram of the fragmented/labelled cRNA was then hybridised to GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Hybridization was performed for 16 hours in accordance with the user manual provided, followed by washing in GeneChip® Fluidics Station 450 (Affymetrix)
| | Sample_scan_protocol | GeneChips were scanned on a GeneChip® Scanner 3000 (Affymetrix) according to the protocol from Affymetrix. GeneChip Command Console Software (AGCC) was used to capture microarray images and quantify signal intensity from each feature.
| | Sample_data_processing | Microarray raw data was acquired using the GCOS software (Affymetrix). Data obtained from GCOS was transferred to GeneSpring GX software (Agilent Technologies, Santa Clara, CA). The data was normalized using the default setting of Genespring. To analyze the data, the genes were grouped according to migratory or non-migratory NSCs towards different tumor attractants. The data was filtered according to their flags in such a way that 3 out of 3 sample replicates fulfilled the conditions of a cut-off of ≥ two-fold difference in expression level and a p-value of less than 0.05. Volcano plot was used to filter the data further.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Can,,Chen
| | Sample_contact_email | a0068186@nus.edu.sg
| | Sample_contact_laboratory | Wang Shu Lab
| | Sample_contact_department | Department of Biological Sciences
| | Sample_contact_institute | National University of Singapore
| | Sample_contact_address | Science Drive 4
| | Sample_contact_city | Singapore
| | Sample_contact_zip/postal_code | 117543
| | Sample_contact_country | Singapore
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000619/suppl/GSM1000619_Migratory_hiPSCs-NSCs_4T1_BiolRep2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000619/suppl/GSM1000619_Migratory_hiPSCs-NSCs_4T1_BiolRep2.CHP.gz
| | Sample_series_id | GSE40750
| | Sample_series_id | GSE40751
| | Sample_data_row_count | 54675
| | |
|
GSM1000620 | GPL570 |
|
Migratory hiPSCs-NSCs towards 4T1, biological rep3
|
hiPSCs-NSCs migrating towards 4T1
|
cell type: human induced pluripotent stem cell-derived neural stem cells
|
Gene expression data from migratory hiPSCs derived NSCs towards 4T1
|
| Sample_geo_accession | GSM1000620
| | Sample_status | Public on Feb 28 2013
| | Sample_submission_date | Sep 10 2012
| | Sample_last_update_date | Feb 28 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Six-well Boyden chambers with 8 μm pore size were utilized for cell separation. hiPSCs-NSCs were seeded at 1 x 106 cells per insert into the upper chamber in 2 ml of Opti-MEM, and the bottom receiver wells were filled with 3 ml of 4T1 cell-conditioned medium as attractants. A total of 24 chambers were seeded for one tumor type. After incubation at 37°C in 5% CO2 for 16 hours, migratory cells on the bottom of the insert membrane and non-migratory cells on the upper side of the membrane were digested by Accutase and collected. Cells collected from 8 wells were combined into one sample.
| | Sample_growth_protocol_ch1 | hiPSCs derived NSCs were cultured on 0.1 Gelatin coated 6 well plates in NSC medium consisting of DMEM/F12, 2% B27, 2 mM L-glutamine, 20 ng/ml human epidermal growth factor (EGF) , 20 ng/ml bFGF (PeproTech) and penicillin/streptomycin. These cells were split every 3 - 4 days by digested with Accutase and plated at a density of 50,000 to 60,000 cells per cm2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a Trizol method (TRIzol® RNeasy Total RNA Purification Kit, Invitrogen) according to the manufacturer’s instructions. Extracted RNA samples were re-suspended in RNase-free water and then treated with RNase-free DNase (QIAGEN) and RNeasy column purification (QIAGEN)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One microgram of isolated total RNAs from each sample was reverse-transcribed, T7-amplified, fragmented and labelled using Kreatech’s RNA ampULSe amplification and labelling kit according to the instruction manual provided (Kreatech Biotechnology, Amsterdam, Netherlands).
| | Sample_hyb_protocol | Fifteen microgram of the fragmented/labelled cRNA was then hybridised to GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Hybridization was performed for 16 hours in accordance with the user manual provided, followed by washing in GeneChip® Fluidics Station 450 (Affymetrix)
| | Sample_scan_protocol | GeneChips were scanned on a GeneChip® Scanner 3000 (Affymetrix) according to the protocol from Affymetrix. GeneChip Command Console Software (AGCC) was used to capture microarray images and quantify signal intensity from each feature.
| | Sample_data_processing | Microarray raw data was acquired using the GCOS software (Affymetrix). Data obtained from GCOS was transferred to GeneSpring GX software (Agilent Technologies, Santa Clara, CA). The data was normalized using the default setting of Genespring. To analyze the data, the genes were grouped according to migratory or non-migratory NSCs towards different tumor attractants. The data was filtered according to their flags in such a way that 3 out of 3 sample replicates fulfilled the conditions of a cut-off of ≥ two-fold difference in expression level and a p-value of less than 0.05. Volcano plot was used to filter the data further.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Can,,Chen
| | Sample_contact_email | a0068186@nus.edu.sg
| | Sample_contact_laboratory | Wang Shu Lab
| | Sample_contact_department | Department of Biological Sciences
| | Sample_contact_institute | National University of Singapore
| | Sample_contact_address | Science Drive 4
| | Sample_contact_city | Singapore
| | Sample_contact_zip/postal_code | 117543
| | Sample_contact_country | Singapore
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000620/suppl/GSM1000620_Migratory_hiPSCs-NSCs_4T1_BiolRep3.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000620/suppl/GSM1000620_Migratory_hiPSCs-NSCs_4T1_BiolRep3.CHP.gz
| | Sample_series_id | GSE40750
| | Sample_series_id | GSE40751
| | Sample_data_row_count | 54675
| | |
|
GSM1000621 | GPL570 |
|
Non-migratory hiPSCs-NSCs towards 4T1, biological rep1
|
hiPSCs-NSCs not migrating towards 4T1
|
cell type: human induced pluripotent stem cell-derived neural stem cells
|
Gene expression data from non-migratory hiPSCs derived NSCs towards 4T1
|
| Sample_geo_accession | GSM1000621
| | Sample_status | Public on Feb 28 2013
| | Sample_submission_date | Sep 10 2012
| | Sample_last_update_date | Feb 28 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Six-well Boyden chambers with 8 μm pore size were utilized for cell separation. hiPSCs-NSCs were seeded at 1 x 106 cells per insert into the upper chamber in 2 ml of Opti-MEM, and the bottom receiver wells were filled with 3 ml of 4T1 cell-conditioned medium as attractants. A total of 24 chambers were seeded for one tumor type. After incubation at 37°C in 5% CO2 for 16 hours, migratory cells on the bottom of the insert membrane and non-migratory cells on the upper side of the membrane were digested by Accutase and collected. Cells collected from 8 wells were combined into one sample.
| | Sample_growth_protocol_ch1 | hiPSCs derived NSCs were cultured on 0.1 Gelatin coated 6 well plates in NSC medium consisting of DMEM/F12, 2% B27, 2 mM L-glutamine, 20 ng/ml human epidermal growth factor (EGF) , 20 ng/ml bFGF (PeproTech) and penicillin/streptomycin. These cells were split every 3 - 4 days by digested with Accutase and plated at a density of 50,000 to 60,000 cells per cm2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a Trizol method (TRIzol® RNeasy Total RNA Purification Kit, Invitrogen) according to the manufacturer’s instructions. Extracted RNA samples were re-suspended in RNase-free water and then treated with RNase-free DNase (QIAGEN) and RNeasy column purification (QIAGEN)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One microgram of isolated total RNAs from each sample was reverse-transcribed, T7-amplified, fragmented and labelled using Kreatech’s RNA ampULSe amplification and labelling kit according to the instruction manual provided (Kreatech Biotechnology, Amsterdam, Netherlands).
| | Sample_hyb_protocol | Fifteen microgram of the fragmented/labelled cRNA was then hybridised to GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Hybridization was performed for 16 hours in accordance with the user manual provided, followed by washing in GeneChip® Fluidics Station 450 (Affymetrix)
| | Sample_scan_protocol | GeneChips were scanned on a GeneChip® Scanner 3000 (Affymetrix) according to the protocol from Affymetrix. GeneChip Command Console Software (AGCC) was used to capture microarray images and quantify signal intensity from each feature.
| | Sample_data_processing | Microarray raw data was acquired using the GCOS software (Affymetrix). Data obtained from GCOS was transferred to GeneSpring GX software (Agilent Technologies, Santa Clara, CA). The data was normalized using the default setting of Genespring. To analyze the data, the genes were grouped according to migratory or non-migratory NSCs towards different tumor attractants. The data was filtered according to their flags in such a way that 3 out of 3 sample replicates fulfilled the conditions of a cut-off of ≥ two-fold difference in expression level and a p-value of less than 0.05. Volcano plot was used to filter the data further.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Can,,Chen
| | Sample_contact_email | a0068186@nus.edu.sg
| | Sample_contact_laboratory | Wang Shu Lab
| | Sample_contact_department | Department of Biological Sciences
| | Sample_contact_institute | National University of Singapore
| | Sample_contact_address | Science Drive 4
| | Sample_contact_city | Singapore
| | Sample_contact_zip/postal_code | 117543
| | Sample_contact_country | Singapore
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000621/suppl/GSM1000621_Non-migratory_hiPSCs-NSCs_4T1_BiolRep1.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000621/suppl/GSM1000621_Non-migratory_hiPSCs-NSCs_4T1_BiolRep1.CHP.gz
| | Sample_series_id | GSE40750
| | Sample_series_id | GSE40751
| | Sample_data_row_count | 54675
| | |
|
GSM1000622 | GPL570 |
|
Non-migratory hiPSCs-NSCs towards 4T1, biological rep2
|
hiPSCs-NSCs not migrating towards 4T1
|
cell type: human induced pluripotent stem cell-derived neural stem cells
|
Gene expression data from non-migratory hiPSCs derived NSCs towards 4T1
|
| Sample_geo_accession | GSM1000622
| | Sample_status | Public on Feb 28 2013
| | Sample_submission_date | Sep 10 2012
| | Sample_last_update_date | Feb 28 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Six-well Boyden chambers with 8 μm pore size were utilized for cell separation. hiPSCs-NSCs were seeded at 1 x 106 cells per insert into the upper chamber in 2 ml of Opti-MEM, and the bottom receiver wells were filled with 3 ml of 4T1 cell-conditioned medium as attractants. A total of 24 chambers were seeded for one tumor type. After incubation at 37°C in 5% CO2 for 16 hours, migratory cells on the bottom of the insert membrane and non-migratory cells on the upper side of the membrane were digested by Accutase and collected. Cells collected from 8 wells were combined into one sample.
| | Sample_growth_protocol_ch1 | hiPSCs derived NSCs were cultured on 0.1 Gelatin coated 6 well plates in NSC medium consisting of DMEM/F12, 2% B27, 2 mM L-glutamine, 20 ng/ml human epidermal growth factor (EGF) , 20 ng/ml bFGF (PeproTech) and penicillin/streptomycin. These cells were split every 3 - 4 days by digested with Accutase and plated at a density of 50,000 to 60,000 cells per cm2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a Trizol method (TRIzol® RNeasy Total RNA Purification Kit, Invitrogen) according to the manufacturer’s instructions. Extracted RNA samples were re-suspended in RNase-free water and then treated with RNase-free DNase (QIAGEN) and RNeasy column purification (QIAGEN)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One microgram of isolated total RNAs from each sample was reverse-transcribed, T7-amplified, fragmented and labelled using Kreatech’s RNA ampULSe amplification and labelling kit according to the instruction manual provided (Kreatech Biotechnology, Amsterdam, Netherlands).
| | Sample_hyb_protocol | Fifteen microgram of the fragmented/labelled cRNA was then hybridised to GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Hybridization was performed for 16 hours in accordance with the user manual provided, followed by washing in GeneChip® Fluidics Station 450 (Affymetrix)
| | Sample_scan_protocol | GeneChips were scanned on a GeneChip® Scanner 3000 (Affymetrix) according to the protocol from Affymetrix. GeneChip Command Console Software (AGCC) was used to capture microarray images and quantify signal intensity from each feature.
| | Sample_data_processing | Microarray raw data was acquired using the GCOS software (Affymetrix). Data obtained from GCOS was transferred to GeneSpring GX software (Agilent Technologies, Santa Clara, CA). The data was normalized using the default setting of Genespring. To analyze the data, the genes were grouped according to migratory or non-migratory NSCs towards different tumor attractants. The data was filtered according to their flags in such a way that 3 out of 3 sample replicates fulfilled the conditions of a cut-off of ≥ two-fold difference in expression level and a p-value of less than 0.05. Volcano plot was used to filter the data further.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Can,,Chen
| | Sample_contact_email | a0068186@nus.edu.sg
| | Sample_contact_laboratory | Wang Shu Lab
| | Sample_contact_department | Department of Biological Sciences
| | Sample_contact_institute | National University of Singapore
| | Sample_contact_address | Science Drive 4
| | Sample_contact_city | Singapore
| | Sample_contact_zip/postal_code | 117543
| | Sample_contact_country | Singapore
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000622/suppl/GSM1000622_Non-migratory_hiPSCs-NSCs_4T1_BiolRep2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000622/suppl/GSM1000622_Non-migratory_hiPSCs-NSCs_4T1_BiolRep2.CHP.gz
| | Sample_series_id | GSE40750
| | Sample_series_id | GSE40751
| | Sample_data_row_count | 54675
| | |
|
GSM1000623 | GPL570 |
|
Non-migratory hiPSCs-NSCs towards 4T1, biological rep3
|
hiPSCs-NSCs not migrating towards 4T1
|
cell type: human induced pluripotent stem cell-derived neural stem cells
|
Gene expression data from non-migratory hiPSCs derived NSCs towards 4T1
|
| Sample_geo_accession | GSM1000623
| | Sample_status | Public on Feb 28 2013
| | Sample_submission_date | Sep 10 2012
| | Sample_last_update_date | Feb 28 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Six-well Boyden chambers with 8 μm pore size were utilized for cell separation. hiPSCs-NSCs were seeded at 1 x 106 cells per insert into the upper chamber in 2 ml of Opti-MEM, and the bottom receiver wells were filled with 3 ml of 4T1 cell-conditioned medium as attractants. A total of 24 chambers were seeded for one tumor type. After incubation at 37°C in 5% CO2 for 16 hours, migratory cells on the bottom of the insert membrane and non-migratory cells on the upper side of the membrane were digested by Accutase and collected. Cells collected from 8 wells were combined into one sample.
| | Sample_growth_protocol_ch1 | hiPSCs derived NSCs were cultured on 0.1 Gelatin coated 6 well plates in NSC medium consisting of DMEM/F12, 2% B27, 2 mM L-glutamine, 20 ng/ml human epidermal growth factor (EGF) , 20 ng/ml bFGF (PeproTech) and penicillin/streptomycin. These cells were split every 3 - 4 days by digested with Accutase and plated at a density of 50,000 to 60,000 cells per cm2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using a Trizol method (TRIzol® RNeasy Total RNA Purification Kit, Invitrogen) according to the manufacturer’s instructions. Extracted RNA samples were re-suspended in RNase-free water and then treated with RNase-free DNase (QIAGEN) and RNeasy column purification (QIAGEN)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | One microgram of isolated total RNAs from each sample was reverse-transcribed, T7-amplified, fragmented and labelled using Kreatech’s RNA ampULSe amplification and labelling kit according to the instruction manual provided (Kreatech Biotechnology, Amsterdam, Netherlands).
| | Sample_hyb_protocol | Fifteen microgram of the fragmented/labelled cRNA was then hybridised to GeneChip® Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Hybridization was performed for 16 hours in accordance with the user manual provided, followed by washing in GeneChip® Fluidics Station 450 (Affymetrix)
| | Sample_scan_protocol | GeneChips were scanned on a GeneChip® Scanner 3000 (Affymetrix) according to the protocol from Affymetrix. GeneChip Command Console Software (AGCC) was used to capture microarray images and quantify signal intensity from each feature.
| | Sample_data_processing | Microarray raw data was acquired using the GCOS software (Affymetrix). Data obtained from GCOS was transferred to GeneSpring GX software (Agilent Technologies, Santa Clara, CA). The data was normalized using the default setting of Genespring. To analyze the data, the genes were grouped according to migratory or non-migratory NSCs towards different tumor attractants. The data was filtered according to their flags in such a way that 3 out of 3 sample replicates fulfilled the conditions of a cut-off of ≥ two-fold difference in expression level and a p-value of less than 0.05. Volcano plot was used to filter the data further.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Can,,Chen
| | Sample_contact_email | a0068186@nus.edu.sg
| | Sample_contact_laboratory | Wang Shu Lab
| | Sample_contact_department | Department of Biological Sciences
| | Sample_contact_institute | National University of Singapore
| | Sample_contact_address | Science Drive 4
| | Sample_contact_city | Singapore
| | Sample_contact_zip/postal_code | 117543
| | Sample_contact_country | Singapore
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000623/suppl/GSM1000623_Non-migratory_hiPSCs-NSCs_4T1_BiolRep3.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1000nnn/GSM1000623/suppl/GSM1000623_Non-migratory_hiPSCs-NSCs_4T1_BiolRep3.CHP.gz
| | Sample_series_id | GSE40750
| | Sample_series_id | GSE40751
| | Sample_data_row_count | 54675
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