Search results for the GEO ID: GSE35642  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM872400 | GPL96 |
|
SK-N-MC 0nM rotenone 1week rep1
|
Neuroepithelioma SK-N-MC cells, not exposed to rotenone, 1 week
|
cell line: SK-N-MC
treatment: 0nM rotenone
time: 1 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 1 week without rotenone
|
| Sample_geo_accession | GSM872400
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872400/suppl/GSM872400_1w0nM-1.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872401 | GPL96 |
|
SK-N-MC 0nM rotenone 1week rep2
|
Neuroepithelioma SK-N-MC cells, not exposed to rotenone, 1 week
|
cell line: SK-N-MC
treatment: 0nM rotenone
time: 1 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 1 week without rotenone
|
| Sample_geo_accession | GSM872401
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872401/suppl/GSM872401_1w0nM-2.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872402 | GPL96 |
|
SK-N-MC 0nM rotenone 1week rep3
|
Neuroepithelioma SK-N-MC cells, not exposed to rotenone, 1 week
|
cell line: SK-N-MC
treatment: 0nM rotenone
time: 1 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 1 week without rotenone
|
| Sample_geo_accession | GSM872402
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872402/suppl/GSM872402_1w0nM-3.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872403 | GPL96 |
|
SK-N-MC 5nM rotenone 1week rep1
|
Neuroepithelioma SK-N-MC cells, exposed to 5 nM rotenone for 1 week
|
cell line: SK-N-MC
treatment: 5nM rotenone
time: 1 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 1 week with 5 nM rotenone
|
| Sample_geo_accession | GSM872403
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872403/suppl/GSM872403_1w5nM-1.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872404 | GPL96 |
|
SK-N-MC 5nM rotenone 1week rep2
|
Neuroepithelioma SK-N-MC cells, exposed to 5 nM rotenone for 1 week
|
cell line: SK-N-MC
treatment: 5nM rotenone
time: 1 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 1 week with 5 nM rotenone
|
| Sample_geo_accession | GSM872404
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872404/suppl/GSM872404_1w5nM-2.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872405 | GPL96 |
|
SK-N-MC 5nM rotenone 1week rep3
|
Neuroepithelioma SK-N-MC cells, exposed to 5 nM rotenone for 1 week
|
cell line: SK-N-MC
treatment: 5nM rotenone
time: 1 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 1 week with 5 nM rotenone
|
| Sample_geo_accession | GSM872405
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872405/suppl/GSM872405_1w5nM-3.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872406 | GPL96 |
|
SK-N-MC 50nM rotenone 1week rep1
|
Neuroepithelioma SK-N-MC cells, exposed to 50 nM rotenone for 1 week
|
cell line: SK-N-MC
treatment: 50nM rotenone
time: 1 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 1 week with 50 nM rotenone
|
| Sample_geo_accession | GSM872406
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872406/suppl/GSM872406_1w50nM-1.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872407 | GPL96 |
|
SK-N-MC 50nM rotenone 1week rep2
|
Neuroepithelioma SK-N-MC cells, exposed to 50 nM rotenone for 1 week
|
cell line: SK-N-MC
treatment: 50nM rotenone
time: 1 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 1 week with 50 nM rotenone
|
| Sample_geo_accession | GSM872407
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872407/suppl/GSM872407_1w50nM-2.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872408 | GPL96 |
|
SK-N-MC 50nM rotenone 1week rep3
|
Neuroepithelioma SK-N-MC cells, exposed to 50 nM rotenone for 1 week
|
cell line: SK-N-MC
treatment: 50nM rotenone
time: 1 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 1 week with 50 nM rotenone
|
| Sample_geo_accession | GSM872408
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872408/suppl/GSM872408_1w50nM-3.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872409 | GPL96 |
|
SK-N-MC 0nM rotenone 4week rep1
|
Neuroepithelioma SK-N-MC cells, not exposed to rotenone, 4 week
|
cell line: SK-N-MC
treatment: 0nM rotenone
time: 4 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 4 weeks without rotenone
|
| Sample_geo_accession | GSM872409
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872409/suppl/GSM872409_4w0nM-1.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872410 | GPL96 |
|
SK-N-MC 0nM rotenone 4week rep2
|
Neuroepithelioma SK-N-MC cells, not exposed to rotenone, 4 week
|
cell line: SK-N-MC
treatment: 0nM rotenone
time: 4 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 4 weeks without rotenone
|
| Sample_geo_accession | GSM872410
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872410/suppl/GSM872410_4w0nM-2.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872411 | GPL96 |
|
SK-N-MC 0nM rotenone 4week rep3
|
Neuroepithelioma SK-N-MC cells, not exposed to rotenone, 4 week
|
cell line: SK-N-MC
treatment: 0nM rotenone
time: 4 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 4 weeks without rotenone
|
| Sample_geo_accession | GSM872411
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872411/suppl/GSM872411_4w0nM-3.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872412 | GPL96 |
|
SK-N-MC 5nM rotenone 4week rep1
|
Neuroepithelioma SK-N-MC cells, exposed to 5 nM rotenone for 4 week
|
cell line: SK-N-MC
treatment: 5nM rotenone
time: 4 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 4 weeks with 5 nM rotenone
|
| Sample_geo_accession | GSM872412
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872412/suppl/GSM872412_4w5nM-1.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872413 | GPL96 |
|
SK-N-MC 5nM rotenone 4week rep2
|
Neuroepithelioma SK-N-MC cells, exposed to 5 nM rotenone for 4 week
|
cell line: SK-N-MC
treatment: 5nM rotenone
time: 4 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 4 weeks with 5 nM rotenone
|
| Sample_geo_accession | GSM872413
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872413/suppl/GSM872413_4w5nM-2.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872414 | GPL96 |
|
SK-N-MC 5nM rotenone 4week rep3
|
Neuroepithelioma SK-N-MC cells, exposed to 5 nM rotenone for 4 week
|
cell line: SK-N-MC
treatment: 5nM rotenone
time: 4 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 4 weeks with 5 nM rotenone
|
| Sample_geo_accession | GSM872414
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872414/suppl/GSM872414_4w5nM-3.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872415 | GPL96 |
|
SK-N-MC 50nM rotenone 4week rep1
|
Neuroepithelioma SK-N-MC cells, exposed to 50 nM rotenone for 4 week
|
cell line: SK-N-MC
treatment: 50nM rotenone
time: 4 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 4 weeks with 50 nM rotenone
|
| Sample_geo_accession | GSM872415
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872415/suppl/GSM872415_4w50nM-1.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872416 | GPL96 |
|
SK-N-MC 50nM rotenone 4week rep2
|
Neuroepithelioma SK-N-MC cells, exposed to 50 nM rotenone for 4 week
|
cell line: SK-N-MC
treatment: 50nM rotenone
time: 4 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 4 weeks with 50 nM rotenone
|
| Sample_geo_accession | GSM872416
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872416/suppl/GSM872416_4w50nM-2.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
|
GSM872417 | GPL96 |
|
SK-N-MC 50nM rotenone 4week rep3
|
Neuroepithelioma SK-N-MC cells, exposed to 50 nM rotenone for 4 week
|
cell line: SK-N-MC
treatment: 50nM rotenone
time: 4 week
|
Gene expression data from neuroepithelioma SK-N-MC cells, grown for 4 weeks with 50 nM rotenone
|
| Sample_geo_accession | GSM872417
| | Sample_status | Public on Aug 09 2012
| | Sample_submission_date | Feb 08 2012
| | Sample_last_update_date | Aug 10 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were treated for 1 and 4 weeks with two different amounts of rotenone or vehicle-treated (0.05 % ethanol). The 5 nM dose is non-lethal for SK-N-MC cells, while the 50 nM dose is more toxic and causes some death of cultured SK-N-MC cells
| | Sample_growth_protocol_ch1 | Cells were maintained in a 5% CO2 environment at 37 °C, in Eagle’s MEM medium with Earle’s salt (Invitrogen, Carlsbad, CA), supplemented with 5.6 mM D-glucose, 2 mM L-glutamine, non-essential amino acids, 50 U/ml penicillin and streptomycin, and 8 % fetal bovine serum (Invitrogen). As sodium pyruvate protects cells against some of the effects of complex I inhibitors like rotenone, it was not used during the course of the experiments.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions. from triplicate experiments from vehicle-treated and from 4 rotenone-treated groups: 1w0nM and 4w0nM (treated for 1 week and 4 weeks with vehicle), 1w5nM and 4w5nM (treated with 5 nM), 1w50nM and 4w50nM (treated with 50 nM).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3).
| | Sample_hyb_protocol | After fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® HG-U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source in the Hewlett-Packard GeneArray Scanner G2500.
| | Sample_data_processing | The data was normalized and used to assess expression indexes and fold changes (FC > 2.0, compared to vehicle-treated controls) using the model-based expression indexes (MBEI) method implemented in dCHIP, ( http://biosun1.harvard.edu/complab/dchip/),
| | Sample_platform_id | GPL96
| | Sample_contact_name | Yofre,,Cabeza-Arvelaiz
| | Sample_contact_email | yofrecabeza@gmail.com
| | Sample_contact_laboratory | CHS 71-295
| | Sample_contact_department | Pathology and Environmental Health Sciences
| | Sample_contact_institute | University of California, Los Angeles
| | Sample_contact_address | 650 Charles E. Young Drive South
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM872nnn/GSM872417/suppl/GSM872417_4w50nM-3.CEL.gz
| | Sample_series_id | GSE35642
| | Sample_data_row_count | 22283
| | |
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