Search results for the GEO ID: GSE18660  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM463596 | GPL1261 |
|
Untreated control ES cells sample 1
|
Embryonic stem cells, CGR8, passage 25
|
cell line: CGR8
strain: SV129
tissue: embryo
morphology: small, tightly packed
cell type: embryonic stem cell (ES cells)
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM463596
| | Sample_status | Public on Jan 03 2011
| | Sample_submission_date | Oct 21 2009
| | Sample_last_update_date | Jan 03 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Dr A Smith, Wellcome Trust Centre for Stem Cell Research, UK
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463596/suppl/GSM463596.CEL.gz
| | Sample_series_id | GSE18660
| | Sample_data_row_count | 45101
| | |
|
GSM463597 | GPL1261 |
|
Untreated control ES cells sample 2
|
Embryonic stem cells, CGR8, passage 26
|
cell line: CGR8
strain: SV129
tissue: embryo
morphology: small, tightly packed
cell type: embryonic stem cell (ES cells)
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM463597
| | Sample_status | Public on Jan 03 2011
| | Sample_submission_date | Oct 21 2009
| | Sample_last_update_date | Jan 03 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Dr A Smith, Wellcome Trust Centre for Stem Cell Research, UK
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463597/suppl/GSM463597.CEL.gz
| | Sample_series_id | GSE18660
| | Sample_data_row_count | 45101
| | |
|
GSM463598 | GPL1261 |
|
Untreated control ES cells sample 3
|
Embryonic stem cells, CGR8, passage 27
|
cell line: CGR8
strain: SV129
tissue: embryo
morphology: small, tightly packed
cell type: embryonic stem cell (ES cells)
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM463598
| | Sample_status | Public on Jan 03 2011
| | Sample_submission_date | Oct 21 2009
| | Sample_last_update_date | Jan 03 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Dr A Smith, Wellcome Trust Centre for Stem Cell Research, UK
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463598/suppl/GSM463598.CEL.gz
| | Sample_series_id | GSE18660
| | Sample_data_row_count | 45101
| | |
|
GSM463599 | GPL1261 |
|
EBIO-treated ES cells sample 1
|
Embryonic stem cells, CGR8, passage 25, treated with EBIO (1mM) for 3 days
|
cell line: CGR8
strain: SV129
tissue: embryo
morphology: small, tightly packed
cell type: embryonic stem cell (ES cells)
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM463599
| | Sample_status | Public on Jan 03 2011
| | Sample_submission_date | Oct 21 2009
| | Sample_last_update_date | Jan 03 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Dr A Smith, Wellcome Trust Centre for Stem Cell Research, UK
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463599/suppl/GSM463599.CEL.gz
| | Sample_series_id | GSE18660
| | Sample_data_row_count | 45101
| | |
|
GSM463600 | GPL1261 |
|
EBIO-treated ES cells sample 2
|
Embryonic stem cells, CGR8, passage 26, treated with EBIO (1mM) for 3 days
|
cell line: CGR8
strain: SV129
tissue: embryo
morphology: small, tightly packed
cell type: embryonic stem cell (ES cells)
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM463600
| | Sample_status | Public on Jan 03 2011
| | Sample_submission_date | Oct 21 2009
| | Sample_last_update_date | Jan 03 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Dr A Smith, Wellcome Trust Centre for Stem Cell Research, UK
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463600/suppl/GSM463600.CEL.gz
| | Sample_series_id | GSE18660
| | Sample_data_row_count | 45101
| | |
|
GSM463601 | GPL1261 |
|
EBIO-treated ES cells sample 3
|
Embryonic stem cells, CGR8, passage 27, treated with EBIO (1mM) for 3 days
|
cell line: CGR8
strain: SV129
tissue: embryo
morphology: small, tightly packed
cell type: embryonic stem cell (ES cells)
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM463601
| | Sample_status | Public on Jan 03 2011
| | Sample_submission_date | Oct 21 2009
| | Sample_last_update_date | Jan 03 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Dr A Smith, Wellcome Trust Centre for Stem Cell Research, UK
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM463nnn/GSM463601/suppl/GSM463601.CEL.gz
| | Sample_series_id | GSE18660
| | Sample_data_row_count | 45101
| | |
|
GSM549070 | GPL1261 |
|
Untreated control differentiated ES cells sample 1
|
ES cells were induced to differentiated in embryoid body (EB) assay for 5 days and then cultured without EBIO for 10 days (Con_day5+10)
|
cell line: CGR8
strain: SV129
tissue: embryo
morphology: small, tightly packed
cell type: differentiated embryonic stem cell (ES cells)
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM549070
| | Sample_status | Public on Jan 03 2011
| | Sample_submission_date | Jun 02 2010
| | Sample_last_update_date | Jan 03 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Dr A Smith, Wellcome Trust Centre for Stem Cell Research, UK
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM549nnn/GSM549070/suppl/GSM549070.CEL.gz
| | Sample_series_id | GSE18660
| | Sample_data_row_count | 45101
| | |
|
GSM549071 | GPL1261 |
|
Untreated control differentiated ES cells sample 2
|
ES cells were induced to differentiated in embryoid body (EB) assay for 5 days and then cultured without EBIO for 10 days (Con_day5+10)
|
cell line: CGR8
strain: SV129
tissue: embryo
morphology: small, tightly packed
cell type: differentiated embryonic stem cell (ES cells)
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM549071
| | Sample_status | Public on Jan 03 2011
| | Sample_submission_date | Jun 02 2010
| | Sample_last_update_date | Jan 03 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Dr A Smith, Wellcome Trust Centre for Stem Cell Research, UK
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM549nnn/GSM549071/suppl/GSM549071.CEL.gz
| | Sample_series_id | GSE18660
| | Sample_data_row_count | 45101
| | |
|
GSM549078 | GPL1261 |
|
EBIO-treated differentiated ES cells sample 1
|
ES cells were induced to differentiated in embryoid body (EB) assay for 5 days and then treated with EBIO for 10 days (EBIO_day5+10)
|
cell line: CGR8
strain: SV129
tissue: embryo
morphology: small, tightly packed
cell type: differentiated embryonic stem cell (ES cells)
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM549078
| | Sample_status | Public on Jan 03 2011
| | Sample_submission_date | Jun 02 2010
| | Sample_last_update_date | Jan 03 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Dr A Smith, Wellcome Trust Centre for Stem Cell Research, UK
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM549nnn/GSM549078/suppl/GSM549078.CEL.gz
| | Sample_series_id | GSE18660
| | Sample_data_row_count | 45101
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GSM549079 | GPL1261 |
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EBIO-treated differentiatedES cells sample 2
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ES cells were induced to differentiated in embryoid body (EB) assay for 5 days and then treated with EBIO for 10 days (EBIO_day5+10)
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cell line: CGR8
strain: SV129
tissue: embryo
morphology: small, tightly packed
cell type: differentiated embryonic stem cell (ES cells)
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM549079
| | Sample_status | Public on Jan 03 2011
| | Sample_submission_date | Jun 02 2010
| | Sample_last_update_date | Jan 03 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Dr A Smith, Wellcome Trust Centre for Stem Cell Research, UK
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM549nnn/GSM549079/suppl/GSM549079.CEL.gz
| | Sample_series_id | GSE18660
| | Sample_data_row_count | 45101
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