Search results for the GEO ID: GSE35841  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM876103 | GPL1355 |
|
AG9 FHH-IPS-A1-rep1
|
FHH rat induced pluripotent stem cells A1
|
background strain: FHH
cell type: induced pluripotent stem (IPS) cells
ssea-1: positive
oct4: positive
nanog: positive
sox2: positive
|
FHH IPS cells, 5 days after passage.
Gene expression interrogating 31099 transcripts.
|
| Sample_geo_accession | GSM876103
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 15 2012
| | Sample_last_update_date | Jul 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rat ES and IPS cells were cultured in 2i medium. Rat EF cells were cultured in MEF medium.
| | Sample_growth_protocol_ch1 | Rat and mouse embryonic fibroblast (EF) cells were prepared from e14.5 embryos (statement of protocol approval from IACUC), and cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% (fetal calf serum) FBS (HyClone), 2 mM L-glutamine, 1% non-essential amino acid, and 0.1 mM 2-mercaptoethanol. Rat IPS cell lines were cultured on Mitomycin C-treated mouse EF cells in knock-out (KO) medium, which contains DMEM with 20% knock out serum (Invitrogen), 2 mM L-glutamine, 1% non-essential amino acid, 0.1 mM 2-mercaptoethanol and 1000U/ml (Leukemia inhibitory factor) LIF (Chemicon).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | About 1,000,000 rat IPS, ES and EF cells were collected and treated by TRIZ reagent for RNA extracting.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified RNA (~100 ng) was amplified/labeled using an Affymetrix Express Kit.
| | Sample_hyb_protocol | RNA from each culture was independently analyzed. Labeled RNA was hybridized to the Affymetrix GeneChip rat genome RG230 plus 2.0 array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and then stained with PE-conjugated streptavidin (Molecular Probes).
| | Sample_scan_protocol | Arrays were scanned using the GeneChip Scanner 3000. Image data were quantified with Affymetrix Expression Console Software.
| | Sample_data_processing | The quantified raw signal intensities were normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/). Analysis of variation (ANOVA) was conducted and false discovery rates (FDR) were determined using Partek Genomics Suite 6.2 (Partek Incorporated). Differentially expressed probe sets were defined as those possessing ANOVA p<0.01, FDR<0.10 and a log2 ratio >1.5 between the compared groups. Ontological pathway analysis was performed with the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov/). Hierarchical clustering was conducted with Genesis software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sheng,,Yang
| | Sample_contact_email | syang@mcw.edu
| | Sample_contact_laboratory | Jacob and Geurt
| | Sample_contact_department | Human and Molecular Genetics Center
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 52336
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM876nnn/GSM876103/suppl/GSM876103.CEL.gz
| | Sample_series_id | GSE35841
| | Sample_data_row_count | 31099
| | |
|
GSM876104 | GPL1355 |
|
AG10 FHH-IPS-A1-rep2
|
FHH rat induced pluripotent stem cells A1
|
background strain: FHH
cell type: induced pluripotent stem (IPS) cells
ssea-1: positive
oct4: positive
nanog: positive
sox2: positive
|
FHH IPS cells, 5 days after passage.
Gene expression interrogating 31099 transcripts.
|
| Sample_geo_accession | GSM876104
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 15 2012
| | Sample_last_update_date | Jul 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rat ES and IPS cells were cultured in 2i medium. Rat EF cells were cultured in MEF medium.
| | Sample_growth_protocol_ch1 | Rat and mouse embryonic fibroblast (EF) cells were prepared from e14.5 embryos (statement of protocol approval from IACUC), and cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% (fetal calf serum) FBS (HyClone), 2 mM L-glutamine, 1% non-essential amino acid, and 0.1 mM 2-mercaptoethanol. Rat IPS cell lines were cultured on Mitomycin C-treated mouse EF cells in knock-out (KO) medium, which contains DMEM with 20% knock out serum (Invitrogen), 2 mM L-glutamine, 1% non-essential amino acid, 0.1 mM 2-mercaptoethanol and 1000U/ml (Leukemia inhibitory factor) LIF (Chemicon).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | About 1,000,000 rat IPS, ES and EF cells were collected and treated by TRIZ reagent for RNA extracting.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified RNA (~100 ng) was amplified/labeled using an Affymetrix Express Kit.
| | Sample_hyb_protocol | RNA from each culture was independently analyzed. Labeled RNA was hybridized to the Affymetrix GeneChip rat genome RG230 plus 2.0 array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and then stained with PE-conjugated streptavidin (Molecular Probes).
| | Sample_scan_protocol | Arrays were scanned using the GeneChip Scanner 3000. Image data were quantified with Affymetrix Expression Console Software.
| | Sample_data_processing | The quantified raw signal intensities were normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/). Analysis of variation (ANOVA) was conducted and false discovery rates (FDR) were determined using Partek Genomics Suite 6.2 (Partek Incorporated). Differentially expressed probe sets were defined as those possessing ANOVA p<0.01, FDR<0.10 and a log2 ratio >1.5 between the compared groups. Ontological pathway analysis was performed with the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov/). Hierarchical clustering was conducted with Genesis software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sheng,,Yang
| | Sample_contact_email | syang@mcw.edu
| | Sample_contact_laboratory | Jacob and Geurt
| | Sample_contact_department | Human and Molecular Genetics Center
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 52336
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM876nnn/GSM876104/suppl/GSM876104.CEL.gz
| | Sample_series_id | GSE35841
| | Sample_data_row_count | 31099
| | |
|
GSM876105 | GPL1355 |
|
AG11 FHH-IPS-A2-rep1
|
FHH rat induced pluripotent stem cells A2
|
background strain: FHH
cell type: induced pluripotent stem (IPS) cells
ssea-1: positive
oct4: positive
nanog: positive
sox2: positive
|
FHH IPS cells, 5 days after passage.
Gene expression interrogating 31099 transcripts.
|
| Sample_geo_accession | GSM876105
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 15 2012
| | Sample_last_update_date | Jul 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rat ES and IPS cells were cultured in 2i medium. Rat EF cells were cultured in MEF medium.
| | Sample_growth_protocol_ch1 | Rat and mouse embryonic fibroblast (EF) cells were prepared from e14.5 embryos (statement of protocol approval from IACUC), and cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% (fetal calf serum) FBS (HyClone), 2 mM L-glutamine, 1% non-essential amino acid, and 0.1 mM 2-mercaptoethanol. Rat IPS cell lines were cultured on Mitomycin C-treated mouse EF cells in knock-out (KO) medium, which contains DMEM with 20% knock out serum (Invitrogen), 2 mM L-glutamine, 1% non-essential amino acid, 0.1 mM 2-mercaptoethanol and 1000U/ml (Leukemia inhibitory factor) LIF (Chemicon).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | About 1,000,000 rat IPS, ES and EF cells were collected and treated by TRIZ reagent for RNA extracting.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified RNA (~100 ng) was amplified/labeled using an Affymetrix Express Kit.
| | Sample_hyb_protocol | RNA from each culture was independently analyzed. Labeled RNA was hybridized to the Affymetrix GeneChip rat genome RG230 plus 2.0 array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and then stained with PE-conjugated streptavidin (Molecular Probes).
| | Sample_scan_protocol | Arrays were scanned using the GeneChip Scanner 3000. Image data were quantified with Affymetrix Expression Console Software.
| | Sample_data_processing | The quantified raw signal intensities were normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/). Analysis of variation (ANOVA) was conducted and false discovery rates (FDR) were determined using Partek Genomics Suite 6.2 (Partek Incorporated). Differentially expressed probe sets were defined as those possessing ANOVA p<0.01, FDR<0.10 and a log2 ratio >1.5 between the compared groups. Ontological pathway analysis was performed with the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov/). Hierarchical clustering was conducted with Genesis software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sheng,,Yang
| | Sample_contact_email | syang@mcw.edu
| | Sample_contact_laboratory | Jacob and Geurt
| | Sample_contact_department | Human and Molecular Genetics Center
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 52336
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM876nnn/GSM876105/suppl/GSM876105.CEL.gz
| | Sample_series_id | GSE35841
| | Sample_data_row_count | 31099
| | |
|
GSM876106 | GPL1355 |
|
AG12 FHH-IPS-A2-rep2
|
FHH rat induced pluripotent stem cells A2
|
background strain: FHH
cell type: induced pluripotent stem (IPS) cells
ssea-1: positive
oct4: positive
nanog: positive
sox2: positive
|
FHH IPS cells, 5 days after passage.
Gene expression interrogating 31099 transcripts.
|
| Sample_geo_accession | GSM876106
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 15 2012
| | Sample_last_update_date | Jul 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rat ES and IPS cells were cultured in 2i medium. Rat EF cells were cultured in MEF medium.
| | Sample_growth_protocol_ch1 | Rat and mouse embryonic fibroblast (EF) cells were prepared from e14.5 embryos (statement of protocol approval from IACUC), and cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% (fetal calf serum) FBS (HyClone), 2 mM L-glutamine, 1% non-essential amino acid, and 0.1 mM 2-mercaptoethanol. Rat IPS cell lines were cultured on Mitomycin C-treated mouse EF cells in knock-out (KO) medium, which contains DMEM with 20% knock out serum (Invitrogen), 2 mM L-glutamine, 1% non-essential amino acid, 0.1 mM 2-mercaptoethanol and 1000U/ml (Leukemia inhibitory factor) LIF (Chemicon).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | About 1,000,000 rat IPS, ES and EF cells were collected and treated by TRIZ reagent for RNA extracting.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified RNA (~100 ng) was amplified/labeled using an Affymetrix Express Kit.
| | Sample_hyb_protocol | RNA from each culture was independently analyzed. Labeled RNA was hybridized to the Affymetrix GeneChip rat genome RG230 plus 2.0 array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and then stained with PE-conjugated streptavidin (Molecular Probes).
| | Sample_scan_protocol | Arrays were scanned using the GeneChip Scanner 3000. Image data were quantified with Affymetrix Expression Console Software.
| | Sample_data_processing | The quantified raw signal intensities were normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/). Analysis of variation (ANOVA) was conducted and false discovery rates (FDR) were determined using Partek Genomics Suite 6.2 (Partek Incorporated). Differentially expressed probe sets were defined as those possessing ANOVA p<0.01, FDR<0.10 and a log2 ratio >1.5 between the compared groups. Ontological pathway analysis was performed with the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov/). Hierarchical clustering was conducted with Genesis software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sheng,,Yang
| | Sample_contact_email | syang@mcw.edu
| | Sample_contact_laboratory | Jacob and Geurt
| | Sample_contact_department | Human and Molecular Genetics Center
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 52336
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM876nnn/GSM876106/suppl/GSM876106.CEL.gz
| | Sample_series_id | GSE35841
| | Sample_data_row_count | 31099
| | |
|
GSM876107 | GPL1355 |
|
AG13 DAC8-rep1
|
rat DAC8 embryonic stem cells
|
cell line: DAC8
cell type: embryonic stem (ES) cells
ssea-1: positive
oct4: positive
nanog: positive
sox2: positive
|
DAC8 ES cells, 5 days after passage.
Gene expression interrogating 31099 transcripts.
|
| Sample_geo_accession | GSM876107
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 15 2012
| | Sample_last_update_date | Jul 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rat ES and IPS cells were cultured in 2i medium. Rat EF cells were cultured in MEF medium.
| | Sample_growth_protocol_ch1 | Rat and mouse embryonic fibroblast (EF) cells were prepared from e14.5 embryos (statement of protocol approval from IACUC), and cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% (fetal calf serum) FBS (HyClone), 2 mM L-glutamine, 1% non-essential amino acid, and 0.1 mM 2-mercaptoethanol. Rat IPS cell lines were cultured on Mitomycin C-treated mouse EF cells in knock-out (KO) medium, which contains DMEM with 20% knock out serum (Invitrogen), 2 mM L-glutamine, 1% non-essential amino acid, 0.1 mM 2-mercaptoethanol and 1000U/ml (Leukemia inhibitory factor) LIF (Chemicon).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | About 1,000,000 rat IPS, ES and EF cells were collected and treated by TRIZ reagent for RNA extracting.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified RNA (~100 ng) was amplified/labeled using an Affymetrix Express Kit.
| | Sample_hyb_protocol | RNA from each culture was independently analyzed. Labeled RNA was hybridized to the Affymetrix GeneChip rat genome RG230 plus 2.0 array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and then stained with PE-conjugated streptavidin (Molecular Probes).
| | Sample_scan_protocol | Arrays were scanned using the GeneChip Scanner 3000. Image data were quantified with Affymetrix Expression Console Software.
| | Sample_data_processing | The quantified raw signal intensities were normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/). Analysis of variation (ANOVA) was conducted and false discovery rates (FDR) were determined using Partek Genomics Suite 6.2 (Partek Incorporated). Differentially expressed probe sets were defined as those possessing ANOVA p<0.01, FDR<0.10 and a log2 ratio >1.5 between the compared groups. Ontological pathway analysis was performed with the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov/). Hierarchical clustering was conducted with Genesis software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sheng,,Yang
| | Sample_contact_email | syang@mcw.edu
| | Sample_contact_laboratory | Jacob and Geurt
| | Sample_contact_department | Human and Molecular Genetics Center
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 52336
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM876nnn/GSM876107/suppl/GSM876107.CEL.gz
| | Sample_series_id | GSE35841
| | Sample_data_row_count | 31099
| | |
|
GSM876108 | GPL1355 |
|
AG14 DAC8-rep2
|
rat DAC8 embryonic stem cells
|
cell line: DAC8
cell type: embryonic stem (ES) cells
ssea-1: positive
oct4: positive
nanog: positive
sox2: positive
|
DAC8 ES cells, 5 days after passage.
Gene expression interrogating 31099 transcripts.
|
| Sample_geo_accession | GSM876108
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 15 2012
| | Sample_last_update_date | Jul 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rat ES and IPS cells were cultured in 2i medium. Rat EF cells were cultured in MEF medium.
| | Sample_growth_protocol_ch1 | Rat and mouse embryonic fibroblast (EF) cells were prepared from e14.5 embryos (statement of protocol approval from IACUC), and cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% (fetal calf serum) FBS (HyClone), 2 mM L-glutamine, 1% non-essential amino acid, and 0.1 mM 2-mercaptoethanol. Rat IPS cell lines were cultured on Mitomycin C-treated mouse EF cells in knock-out (KO) medium, which contains DMEM with 20% knock out serum (Invitrogen), 2 mM L-glutamine, 1% non-essential amino acid, 0.1 mM 2-mercaptoethanol and 1000U/ml (Leukemia inhibitory factor) LIF (Chemicon).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | About 1,000,000 rat IPS, ES and EF cells were collected and treated by TRIZ reagent for RNA extracting.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified RNA (~100 ng) was amplified/labeled using an Affymetrix Express Kit.
| | Sample_hyb_protocol | RNA from each culture was independently analyzed. Labeled RNA was hybridized to the Affymetrix GeneChip rat genome RG230 plus 2.0 array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and then stained with PE-conjugated streptavidin (Molecular Probes).
| | Sample_scan_protocol | Arrays were scanned using the GeneChip Scanner 3000. Image data were quantified with Affymetrix Expression Console Software.
| | Sample_data_processing | The quantified raw signal intensities were normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/). Analysis of variation (ANOVA) was conducted and false discovery rates (FDR) were determined using Partek Genomics Suite 6.2 (Partek Incorporated). Differentially expressed probe sets were defined as those possessing ANOVA p<0.01, FDR<0.10 and a log2 ratio >1.5 between the compared groups. Ontological pathway analysis was performed with the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov/). Hierarchical clustering was conducted with Genesis software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sheng,,Yang
| | Sample_contact_email | syang@mcw.edu
| | Sample_contact_laboratory | Jacob and Geurt
| | Sample_contact_department | Human and Molecular Genetics Center
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 52336
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM876nnn/GSM876108/suppl/GSM876108.CEL.gz
| | Sample_series_id | GSE35841
| | Sample_data_row_count | 31099
| | |
|
GSM876109 | GPL1355 |
|
AG15 FHH-REF1-rep1
|
FHH rat embryonic fibroblast cell 1
|
background strain: FHH
age: e14.5
cell type: embryonic fibroblast (EF) cells
morphology: same as mouse embryonic fibroblast cells
|
FHH rat embryonic fibroblast cells, 6 days after passage.
Gene expression interrogating 31099 transcripts.
|
| Sample_geo_accession | GSM876109
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 15 2012
| | Sample_last_update_date | Jul 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rat ES and IPS cells were cultured in 2i medium. Rat EF cells were cultured in MEF medium.
| | Sample_growth_protocol_ch1 | Rat and mouse embryonic fibroblast (EF) cells were prepared from e14.5 embryos (statement of protocol approval from IACUC), and cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% (fetal calf serum) FBS (HyClone), 2 mM L-glutamine, 1% non-essential amino acid, and 0.1 mM 2-mercaptoethanol. Rat IPS cell lines were cultured on Mitomycin C-treated mouse EF cells in knock-out (KO) medium, which contains DMEM with 20% knock out serum (Invitrogen), 2 mM L-glutamine, 1% non-essential amino acid, 0.1 mM 2-mercaptoethanol and 1000U/ml (Leukemia inhibitory factor) LIF (Chemicon).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | About 1,000,000 rat IPS, ES and EF cells were collected and treated by TRIZ reagent for RNA extracting.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified RNA (~100 ng) was amplified/labeled using an Affymetrix Express Kit.
| | Sample_hyb_protocol | RNA from each culture was independently analyzed. Labeled RNA was hybridized to the Affymetrix GeneChip rat genome RG230 plus 2.0 array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and then stained with PE-conjugated streptavidin (Molecular Probes).
| | Sample_scan_protocol | Arrays were scanned using the GeneChip Scanner 3000. Image data were quantified with Affymetrix Expression Console Software.
| | Sample_data_processing | The quantified raw signal intensities were normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/). Analysis of variation (ANOVA) was conducted and false discovery rates (FDR) were determined using Partek Genomics Suite 6.2 (Partek Incorporated). Differentially expressed probe sets were defined as those possessing ANOVA p<0.01, FDR<0.10 and a log2 ratio >1.5 between the compared groups. Ontological pathway analysis was performed with the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov/). Hierarchical clustering was conducted with Genesis software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sheng,,Yang
| | Sample_contact_email | syang@mcw.edu
| | Sample_contact_laboratory | Jacob and Geurt
| | Sample_contact_department | Human and Molecular Genetics Center
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 52336
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM876nnn/GSM876109/suppl/GSM876109.CEL.gz
| | Sample_series_id | GSE35841
| | Sample_data_row_count | 31099
| | |
|
GSM876110 | GPL1355 |
|
AG16 FHH-REF1-rep2
|
FHH rat embryonic fibroblast cell 1
|
background strain: FHH
age: e14.5
cell type: embryonic fibroblast (EF) cells
morphology: same as mouse embryonic fibroblast cells
|
FHH rat embryonic fibroblast cells, 6 days after passage.
Gene expression interrogating 31099 transcripts.
|
| Sample_geo_accession | GSM876110
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 15 2012
| | Sample_last_update_date | Jul 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rat ES and IPS cells were cultured in 2i medium. Rat EF cells were cultured in MEF medium.
| | Sample_growth_protocol_ch1 | Rat and mouse embryonic fibroblast (EF) cells were prepared from e14.5 embryos (statement of protocol approval from IACUC), and cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% (fetal calf serum) FBS (HyClone), 2 mM L-glutamine, 1% non-essential amino acid, and 0.1 mM 2-mercaptoethanol. Rat IPS cell lines were cultured on Mitomycin C-treated mouse EF cells in knock-out (KO) medium, which contains DMEM with 20% knock out serum (Invitrogen), 2 mM L-glutamine, 1% non-essential amino acid, 0.1 mM 2-mercaptoethanol and 1000U/ml (Leukemia inhibitory factor) LIF (Chemicon).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | About 1,000,000 rat IPS, ES and EF cells were collected and treated by TRIZ reagent for RNA extracting.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified RNA (~100 ng) was amplified/labeled using an Affymetrix Express Kit.
| | Sample_hyb_protocol | RNA from each culture was independently analyzed. Labeled RNA was hybridized to the Affymetrix GeneChip rat genome RG230 plus 2.0 array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and then stained with PE-conjugated streptavidin (Molecular Probes).
| | Sample_scan_protocol | Arrays were scanned using the GeneChip Scanner 3000. Image data were quantified with Affymetrix Expression Console Software.
| | Sample_data_processing | The quantified raw signal intensities were normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/). Analysis of variation (ANOVA) was conducted and false discovery rates (FDR) were determined using Partek Genomics Suite 6.2 (Partek Incorporated). Differentially expressed probe sets were defined as those possessing ANOVA p<0.01, FDR<0.10 and a log2 ratio >1.5 between the compared groups. Ontological pathway analysis was performed with the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov/). Hierarchical clustering was conducted with Genesis software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sheng,,Yang
| | Sample_contact_email | syang@mcw.edu
| | Sample_contact_laboratory | Jacob and Geurt
| | Sample_contact_department | Human and Molecular Genetics Center
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 52336
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM876nnn/GSM876110/suppl/GSM876110.CEL.gz
| | Sample_series_id | GSE35841
| | Sample_data_row_count | 31099
| | |
|
GSM876111 | GPL1355 |
|
AG17 FHH-REF2-rep1
|
FHH rat embryonic fibroblast cell 2
|
background strain: FHH
age: e14.5
cell type: embryonic fibroblast (EF) cells
morphology: same as mouse embryonic fibroblast cells
|
FHH rat embryonic fibroblast cells, 6 days after passage.
Gene expression interrogating 31099 transcripts.
|
| Sample_geo_accession | GSM876111
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 15 2012
| | Sample_last_update_date | Jul 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rat ES and IPS cells were cultured in 2i medium. Rat EF cells were cultured in MEF medium.
| | Sample_growth_protocol_ch1 | Rat and mouse embryonic fibroblast (EF) cells were prepared from e14.5 embryos (statement of protocol approval from IACUC), and cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% (fetal calf serum) FBS (HyClone), 2 mM L-glutamine, 1% non-essential amino acid, and 0.1 mM 2-mercaptoethanol. Rat IPS cell lines were cultured on Mitomycin C-treated mouse EF cells in knock-out (KO) medium, which contains DMEM with 20% knock out serum (Invitrogen), 2 mM L-glutamine, 1% non-essential amino acid, 0.1 mM 2-mercaptoethanol and 1000U/ml (Leukemia inhibitory factor) LIF (Chemicon).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | About 1,000,000 rat IPS, ES and EF cells were collected and treated by TRIZ reagent for RNA extracting.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified RNA (~100 ng) was amplified/labeled using an Affymetrix Express Kit.
| | Sample_hyb_protocol | RNA from each culture was independently analyzed. Labeled RNA was hybridized to the Affymetrix GeneChip rat genome RG230 plus 2.0 array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and then stained with PE-conjugated streptavidin (Molecular Probes).
| | Sample_scan_protocol | Arrays were scanned using the GeneChip Scanner 3000. Image data were quantified with Affymetrix Expression Console Software.
| | Sample_data_processing | The quantified raw signal intensities were normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/). Analysis of variation (ANOVA) was conducted and false discovery rates (FDR) were determined using Partek Genomics Suite 6.2 (Partek Incorporated). Differentially expressed probe sets were defined as those possessing ANOVA p<0.01, FDR<0.10 and a log2 ratio >1.5 between the compared groups. Ontological pathway analysis was performed with the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov/). Hierarchical clustering was conducted with Genesis software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sheng,,Yang
| | Sample_contact_email | syang@mcw.edu
| | Sample_contact_laboratory | Jacob and Geurt
| | Sample_contact_department | Human and Molecular Genetics Center
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 52336
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM876nnn/GSM876111/suppl/GSM876111.CEL.gz
| | Sample_series_id | GSE35841
| | Sample_data_row_count | 31099
| | |
|
GSM876112 | GPL1355 |
|
AG18 FHH-REF2-rep2
|
FHH rat embryonic fibroblast cell 2
|
background strain: FHH
age: e14.5
cell type: embryonic fibroblast (EF) cells
morphology: same as mouse embryonic fibroblast cells
|
FHH rat embryonic fibroblast cells, 6 days after passage.
Gene expression interrogating 31099 transcripts.
|
| Sample_geo_accession | GSM876112
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 15 2012
| | Sample_last_update_date | Jul 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rat ES and IPS cells were cultured in 2i medium. Rat EF cells were cultured in MEF medium.
| | Sample_growth_protocol_ch1 | Rat and mouse embryonic fibroblast (EF) cells were prepared from e14.5 embryos (statement of protocol approval from IACUC), and cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% (fetal calf serum) FBS (HyClone), 2 mM L-glutamine, 1% non-essential amino acid, and 0.1 mM 2-mercaptoethanol. Rat IPS cell lines were cultured on Mitomycin C-treated mouse EF cells in knock-out (KO) medium, which contains DMEM with 20% knock out serum (Invitrogen), 2 mM L-glutamine, 1% non-essential amino acid, 0.1 mM 2-mercaptoethanol and 1000U/ml (Leukemia inhibitory factor) LIF (Chemicon).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | About 1,000,000 rat IPS, ES and EF cells were collected and treated by TRIZ reagent for RNA extracting.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified RNA (~100 ng) was amplified/labeled using an Affymetrix Express Kit.
| | Sample_hyb_protocol | RNA from each culture was independently analyzed. Labeled RNA was hybridized to the Affymetrix GeneChip rat genome RG230 plus 2.0 array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and then stained with PE-conjugated streptavidin (Molecular Probes).
| | Sample_scan_protocol | Arrays were scanned using the GeneChip Scanner 3000. Image data were quantified with Affymetrix Expression Console Software.
| | Sample_data_processing | The quantified raw signal intensities were normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/). Analysis of variation (ANOVA) was conducted and false discovery rates (FDR) were determined using Partek Genomics Suite 6.2 (Partek Incorporated). Differentially expressed probe sets were defined as those possessing ANOVA p<0.01, FDR<0.10 and a log2 ratio >1.5 between the compared groups. Ontological pathway analysis was performed with the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov/). Hierarchical clustering was conducted with Genesis software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sheng,,Yang
| | Sample_contact_email | syang@mcw.edu
| | Sample_contact_laboratory | Jacob and Geurt
| | Sample_contact_department | Human and Molecular Genetics Center
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 52336
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM876nnn/GSM876112/suppl/GSM876112.CEL.gz
| | Sample_series_id | GSE35841
| | Sample_data_row_count | 31099
| | |
|
GSM876113 | GPL1355 |
|
AG23 DAC2-rep1
|
rat DAC2 embryonic stem cells
|
cell line: DAC2
cell type: embryonic stem (ES) cells
ssea-1: positive
oct4: positive
nanog: positive
sox2: positive
|
DAC2 ES cells, 5 days after passage.
Gene expression interrogating 31099 transcripts.
|
| Sample_geo_accession | GSM876113
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 15 2012
| | Sample_last_update_date | Jul 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rat ES and IPS cells were cultured in 2i medium. Rat EF cells were cultured in MEF medium.
| | Sample_growth_protocol_ch1 | Rat and mouse embryonic fibroblast (EF) cells were prepared from e14.5 embryos (statement of protocol approval from IACUC), and cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% (fetal calf serum) FBS (HyClone), 2 mM L-glutamine, 1% non-essential amino acid, and 0.1 mM 2-mercaptoethanol. Rat IPS cell lines were cultured on Mitomycin C-treated mouse EF cells in knock-out (KO) medium, which contains DMEM with 20% knock out serum (Invitrogen), 2 mM L-glutamine, 1% non-essential amino acid, 0.1 mM 2-mercaptoethanol and 1000U/ml (Leukemia inhibitory factor) LIF (Chemicon).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | About 1,000,000 rat IPS, ES and EF cells were collected and treated by TRIZ reagent for RNA extracting.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified RNA (~100 ng) was amplified/labeled using an Affymetrix Express Kit.
| | Sample_hyb_protocol | RNA from each culture was independently analyzed. Labeled RNA was hybridized to the Affymetrix GeneChip rat genome RG230 plus 2.0 array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and then stained with PE-conjugated streptavidin (Molecular Probes).
| | Sample_scan_protocol | Arrays were scanned using the GeneChip Scanner 3000. Image data were quantified with Affymetrix Expression Console Software.
| | Sample_data_processing | The quantified raw signal intensities were normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/). Analysis of variation (ANOVA) was conducted and false discovery rates (FDR) were determined using Partek Genomics Suite 6.2 (Partek Incorporated). Differentially expressed probe sets were defined as those possessing ANOVA p<0.01, FDR<0.10 and a log2 ratio >1.5 between the compared groups. Ontological pathway analysis was performed with the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov/). Hierarchical clustering was conducted with Genesis software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sheng,,Yang
| | Sample_contact_email | syang@mcw.edu
| | Sample_contact_laboratory | Jacob and Geurt
| | Sample_contact_department | Human and Molecular Genetics Center
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 52336
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM876nnn/GSM876113/suppl/GSM876113.CEL.gz
| | Sample_series_id | GSE35841
| | Sample_data_row_count | 31099
| | |
|
GSM876114 | GPL1355 |
|
AG24 DAC2-rep2
|
rat DAC2 embryonic stem cells
|
cell line: DAC2
cell type: embryonic stem (ES) cells
ssea-1: positive
oct4: positive
nanog: positive
sox2: positive
|
DAC2 ES cells, 5 days after passage.
Gene expression interrogating 31099 transcripts.
|
| Sample_geo_accession | GSM876114
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 15 2012
| | Sample_last_update_date | Jul 29 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rat ES and IPS cells were cultured in 2i medium. Rat EF cells were cultured in MEF medium.
| | Sample_growth_protocol_ch1 | Rat and mouse embryonic fibroblast (EF) cells were prepared from e14.5 embryos (statement of protocol approval from IACUC), and cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% (fetal calf serum) FBS (HyClone), 2 mM L-glutamine, 1% non-essential amino acid, and 0.1 mM 2-mercaptoethanol. Rat IPS cell lines were cultured on Mitomycin C-treated mouse EF cells in knock-out (KO) medium, which contains DMEM with 20% knock out serum (Invitrogen), 2 mM L-glutamine, 1% non-essential amino acid, 0.1 mM 2-mercaptoethanol and 1000U/ml (Leukemia inhibitory factor) LIF (Chemicon).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | About 1,000,000 rat IPS, ES and EF cells were collected and treated by TRIZ reagent for RNA extracting.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Purified RNA (~100 ng) was amplified/labeled using an Affymetrix Express Kit.
| | Sample_hyb_protocol | RNA from each culture was independently analyzed. Labeled RNA was hybridized to the Affymetrix GeneChip rat genome RG230 plus 2.0 array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and then stained with PE-conjugated streptavidin (Molecular Probes).
| | Sample_scan_protocol | Arrays were scanned using the GeneChip Scanner 3000. Image data were quantified with Affymetrix Expression Console Software.
| | Sample_data_processing | The quantified raw signal intensities were normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/). Analysis of variation (ANOVA) was conducted and false discovery rates (FDR) were determined using Partek Genomics Suite 6.2 (Partek Incorporated). Differentially expressed probe sets were defined as those possessing ANOVA p<0.01, FDR<0.10 and a log2 ratio >1.5 between the compared groups. Ontological pathway analysis was performed with the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov/). Hierarchical clustering was conducted with Genesis software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sheng,,Yang
| | Sample_contact_email | syang@mcw.edu
| | Sample_contact_laboratory | Jacob and Geurt
| | Sample_contact_department | Human and Molecular Genetics Center
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 52336
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM876nnn/GSM876114/suppl/GSM876114.CEL.gz
| | Sample_series_id | GSE35841
| | Sample_data_row_count | 31099
| | |
|
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