Search results for the GEO ID: GSE16157  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM405147 | GPL570 |
|
HT-1080_2DG+Met
|
HT-1080_2DG+Met, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: 2DG
inhibitor: Met
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Cont-3vsCont_select.CHP(HT-1080_ctrl#3)
|
| Sample_geo_accession | GSM405147
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405147/suppl/GSM405147.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405147/suppl/GSM405147.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405148 | GPL570 |
|
HT-1080_2DG+Bu
|
HT-1080_2DG+Bu, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: 2DG
inhibitor: Bu
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Cont-3vsCont_select.CHP(HT-1080_ctrl#3)
|
| Sample_geo_accession | GSM405148
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405148/suppl/GSM405148.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405148/suppl/GSM405148.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405149 | GPL570 |
|
HT-1080_2DG+Phen
|
HT-1080_2DG+Phen, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: 2DG
inhibitor: Phen
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Cont-3vsCont_select.CHP(HT-1080_ctrl#3)
|
| Sample_geo_accession | GSM405149
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405149/suppl/GSM405149.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405149/suppl/GSM405149.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405150 | GPL570 |
|
HT-1080_2DG+VST
|
HT-1080_2DG+VST, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: 2DG
inhibitor: VST
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Cont-3vsCont_select.CHP(HT-1080_ctrl#3)
|
| Sample_geo_accession | GSM405150
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405150/suppl/GSM405150.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405150/suppl/GSM405150.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405151 | GPL570 |
|
HT-1080_2DG+Rot
|
HT-1080_2DG+Rot, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: 2DG
inhibitor: Rot
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Cont-4vsCont_select.CHP(HT-1080_ctrl#4)
|
| Sample_geo_accession | GSM405151
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405151/suppl/GSM405151.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405151/suppl/GSM405151.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405152 | GPL570 |
|
HT-1080(rho0)_2DG
|
HT-1080(rho0)_2DG, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: deficient
stress: 2DG
inhibitor: none
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_rho0_Cont.CHP(HT-1080(rho0)_ctrl#1)
|
| Sample_geo_accession | GSM405152
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405152/suppl/GSM405152.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405152/suppl/GSM405152.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405153 | GPL570 |
|
HT-1080_2DG+AA
|
HT-1080_2DG+AA, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: 2DG
inhibitor: AA
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Cont-4vsCont_select.CHP(HT-1080_ctrl#4)
|
| Sample_geo_accession | GSM405153
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405153/suppl/GSM405153.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405153/suppl/GSM405153.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405154 | GPL570 |
|
HT-1080_GS+VST
|
HT-1080_GS+VST, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: GS
inhibitor: VST
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Cont.CHP(HT-1080_ctrl#1)
|
| Sample_geo_accession | GSM405154
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405154/suppl/GSM405154.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405154/suppl/GSM405154.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405156 | GPL570 |
|
HT-1080(rho0)_GS_S
|
HT-1080(rho0)_GS_S, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: deficient
stress: GS
inhibitor: none
time: 18h
supernatant: yes
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_rho0_Cont-2vsrho0_Cont_select.CHP(HT-1080(rho0)_ctrl#2)
|
| Sample_geo_accession | GSM405156
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405156/suppl/GSM405156.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405156/suppl/GSM405156.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405157 | GPL570 |
|
HT-1080_GS+Rot
|
HT-1080_GS+Rot, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: GS
inhibitor: Rot
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Pt_Cont-3vsCont_select.CHP(HT-1080_ctrl#6)
|
| Sample_geo_accession | GSM405157
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405157/suppl/GSM405157.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405157/suppl/GSM405157.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405158 | GPL570 |
|
HT-1080_GS+Rot_S
|
HT-1080_GS+Rot_S, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: GS
inhibitor: Rot
time: 18h
supernatant: yes
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Pt_Cont-3vsCont_select.CHP(HT-1080_ctrl#6)
|
| Sample_geo_accession | GSM405158
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405158/suppl/GSM405158.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405158/suppl/GSM405158.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405159 | GPL570 |
|
HT-1080_GS+AA_S
|
HT-1080_GS+AA_S, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: GS
inhibitor: AA
time: 18h
supernatant: yes
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Pt_Cont-3vsCont_select.CHP(HT-1080_ctrl#6)
|
| Sample_geo_accession | GSM405159
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405159/suppl/GSM405159.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405159/suppl/GSM405159.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405160 | GPL570 |
|
HT-29(rho0)_GS
|
HT-29(rho0)_GS, 14h
|
disease: colorectal adenocarcinoma
cell line: HT-29
mtdna: deficient
stress: GS
inhibitor: none
time: 14h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT-29_rho0_Cont.CHP(HT-29(rho0)_ctrl#1)
|
| Sample_geo_accession | GSM405160
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405160/suppl/GSM405160.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405160/suppl/GSM405160.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405161 | GPL570 |
|
HT-1080_2DG#1
|
HT-1080_2DG#1, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: 2DG
inhibitor: none
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Cont-2vsCont_select.CHP(HT-1080_ctrl#2)
|
| Sample_geo_accession | GSM405161
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405161/suppl/GSM405161.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405161/suppl/GSM405161.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405162 | GPL570 |
|
HT-1080_2DG#2
|
HT-1080_2DG#2, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: 2DG
inhibitor: none
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Cont-4vsCont_select.CHP(HT-1080_ctrl#4)
|
| Sample_geo_accession | GSM405162
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405162/suppl/GSM405162.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405162/suppl/GSM405162.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405163 | GPL570 |
|
HT-1080_2DG#3
|
HT-1080_2DG#3, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: 2DG
inhibitor: none
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Pt_Cont_vsCont_select.CHP(HT-1080_ctrl#5)
|
| Sample_geo_accession | GSM405163
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405163/suppl/GSM405163.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405163/suppl/GSM405163.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405164 | GPL570 |
|
HT-1080_GS#2
|
HT-1080_GS#2, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: GS
inhibitor: none
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Pt_Cont-3vsCont_select.CHP(HT-1080_ctrl#6)
|
| Sample_geo_accession | GSM405164
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405164/suppl/GSM405164.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405164/suppl/GSM405164.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405165 | GPL570 |
|
HT-1080_TM
|
HT-1080_TM, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: TM
inhibitor: none
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Pt_Cont-3vsCont_select.CHP(HT-1080_ctrl#6)
|
| Sample_geo_accession | GSM405165
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405165/suppl/GSM405165.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405165/suppl/GSM405165.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405166 | GPL570 |
|
HT-1080(rho0)_TM
|
HT-1080(rho0)_TM, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: deficient
stress: TM
inhibitor: none
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_rho0_Cont-2vsrho0_Cont_select.CHP(HT-1080(rho0)_ctrl#2)
|
| Sample_geo_accession | GSM405166
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405166/suppl/GSM405166.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405166/suppl/GSM405166.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405167 | GPL570 |
|
HT-1080_TM+Rot
|
HT-1080_TM+Rot, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: TM
inhibitor: Rot
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Pt_Cont-3vsCont_select.CHP(HT-1080_ctrl#6)
|
| Sample_geo_accession | GSM405167
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405167/suppl/GSM405167.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405167/suppl/GSM405167.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405168 | GPL570 |
|
HT-1080_TM+AA
|
HT-1080_TM+AA, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: TM
inhibitor: AA
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Pt_Cont-3vsCont_select.CHP(HT-1080_ctrl#6)
|
| Sample_geo_accession | GSM405168
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405168/suppl/GSM405168.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405168/suppl/GSM405168.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405169 | GPL570 |
|
HT-1080_GS#1
|
HT-1080_GS#1, 18h
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: GS
inhibitor: none
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT1080_Cont.CHP(HT-1080_ctrl#1)
|
| Sample_geo_accession | GSM405169
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405169/suppl/GSM405169.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405169/suppl/GSM405169.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405170 | GPL570 |
|
HT-29_GS#1
|
HT-29_GS#1, 18h
|
disease: colorectal adenocarcinoma
cell line: HT-29
mtdna: present
stress: GS
inhibitor: none
time: 18h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT-29_Cont.CHP(HT-29_ctrl#1)
|
| Sample_geo_accession | GSM405170
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405170/suppl/GSM405170.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405170/suppl/GSM405170.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405172 | GPL570 |
|
HT-29_GS#3
|
HT-29_GS#3, 14h
|
disease: colorectal adenocarcinoma
cell line: HT-29
mtdna: present
stress: GS
inhibitor: none
time: 14h
|
Gene expression data from human cancer cell lines. Corresponding control data set is UPR_HT-29_Pt_ContvsCont_select_Signal.CHP(HT-29_ctrl#3)
|
| Sample_geo_accession | GSM405172
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405172/suppl/GSM405172.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405172/suppl/GSM405172.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405175 | GPL570 |
|
HT-1080_ctrl#3
|
HT-1080_ctrl#3
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: control
inhibitor: control
time: control
|
Gene expression data from human cancer cell lines. Control experiment.
|
| Sample_geo_accession | GSM405175
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405175/suppl/GSM405175.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405175/suppl/GSM405175.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405177 | GPL570 |
|
HT-1080_ctrl#5
|
HT-1080_ctrl#5
|
disease: fibrosarcoma
cell line: HT-1080
mtdna: present
stress: control
inhibitor: control
time: control
|
Gene expression data from human cancer cell lines. Control experiment.
|
| Sample_geo_accession | GSM405177
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405177/suppl/GSM405177.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405177/suppl/GSM405177.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
| | |
|
GSM405181 | GPL570 |
|
HT-29_ctrl#1
|
HT-29_ctrl#1
|
disease: colorectal adenocarcinoma
cell line: HT-29
mtdna: present
stress: control
inhibitor: control
time: control
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Gene expression data from human cancer cell lines. Control experiment.
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| Sample_geo_accession | GSM405181
| | Sample_status | Public on May 14 2010
| | Sample_submission_date | May 19 2009
| | Sample_last_update_date | May 21 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HT-1080 or HT-29 cells were exposed to stress with or without inhibitor (3 microM VST, 10 mM Met, 300 microM Bu, 100 microM Phen, 100 nM Rot, 10 ng/ml of AA) for 18 hours. (GS-treated rho0-HT-29 and corresponding rho+-HT-29 (HT-29/GS#3) were exposed to GS for 14 hours because rho0-HT-29 was severely damaged by 18-hour exposure.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Selected Probe Sets as normalization method. Probes with low (less than 100) signal intensity in all arrays were excluded.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Naomi,,Haga
| | Sample_contact_laboratory | Division of Genome Research
| | Sample_contact_department | Cancer Chemotherapy Center
| | Sample_contact_institute | Japanese Foundation for Cancer Research
| | Sample_contact_address | 3-10-6 Ariake, Koto-ku
| | Sample_contact_city | Tokyo
| | Sample_contact_zip/postal_code | 135-8550
| | Sample_contact_country | Japan
| | Sample_contact_web_link | http://www.jfcr.or.jp/laboratory/english/ccc/genom/index.html
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405181/suppl/GSM405181.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM405nnn/GSM405181/suppl/GSM405181.CHP.gz
| | Sample_series_id | GSE16157
| | Sample_data_row_count | 54675
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