Result

Search results for the GEO ID: GSE23882

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GSM587817

GPL570

Control_MFP_24hr_rep1

Control stable cells, mifepristone (5 nM) treatment, 24 hr

cell line: colon cancer cell line HCT116 clone: Control stable clone agent: mifepristone dose: 5 nM time: 24 hr

cells: Inducible control stable clone established from HCT116 colon cancer cells using the GeneSwitch system. stably integrated plasmids: pSwitch (Invitrogen, Carlsbad, CA, USA), pGene/V5 (Invitrogen) inducible protein: None. inducer: mifepristone (5 nM), 24 hr

Sample_geo_accession	GSM587817
Sample_status	Public on Aug 15 2011
Sample_submission_date	Aug 27 2010
Sample_last_update_date	Aug 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	Established from Dr. Shun-Yuan Jiang’s laboratory.
Sample_treatment_protocol_ch1	Inducible TIG1A, TIG1B, and control stable HCT116 clones were plated in 10-cm dishes overnight in growth medium, and then refreshed with medium containing 5 nM MFP for 24 h. Cells were washed twice with ice-cold PBS and harvested using cell lifter.
Sample_growth_protocol_ch1	culture medium: McCoy’s 5A medium supplemented with 25 mM HEPES, 26 mM NaHCO3, 2 mM L-glutamine, 100 units/ml penicillin, 100 micro g/ml streptomycin, 10% fetal bovine serum, 400 micro g/ml hygromycin and 125 micro g/ml zeocin.
Sample_growth_protocol_ch1	culture conduction: at 37ºC with 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using the RNeasy system (Qiagen, Valencia, CA, USA). The integrity of the total RNA was assessed using a 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA), and RNA integrity values reached more than 9.7 in all tested samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
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 Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with GeneChip® Operating Software v1.4 (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_data_processing	Gene expression data underwent secondary analysis using the GeneSpring GX program (Agilent Technologies, Santa Clara, CA, USA). Data were filtered based on both Detection Call and Signal Log Ratio in any of the comparisons between groups (control and TIG1A or control and TIG1B). Data declared “Absent” in all samples were filtered out. Samples had to be declared “Present” in at least two of three chips within a group to be maintained within the set. The log base 2.0 of the fold change was used as an additional filter. Filtered genes identified to be differentially expressed by 2-fold or greater in two of three chips were analyzed for functional gene clusters using GeneSpring. Statistical analyses were performed using one way ANOVA (p<0.05) and t-tests.
Sample_platform_id	GPL570
Sample_contact_name	Shun-Yuan,,Jiang
Sample_contact_department	Department of Research
Sample_contact_institute	Buddhist Tzu Chi General Hospital, Taipei Branch
Sample_contact_address	289 Jianguo Rd
Sample_contact_city	Sindian City
Sample_contact_state	Taipei county
Sample_contact_zip/postal_code	231
Sample_contact_country	Taiwan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587817/suppl/GSM587817.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587817/suppl/GSM587817.CHP.gz
Sample_series_id	GSE23882
Sample_data_row_count	54675

GSM587818

GPL570

Control_MFP_24hr_rep2

Control stable cells, mifepristone (5 nM) treatment, 24 hr.

cell line: colon cancer cell line HCT116 clone: Control stable clone agent: mifepristone dose: 5 nM time: 24 hr

Sample_geo_accession	GSM587818
Sample_status	Public on Aug 15 2011
Sample_submission_date	Aug 27 2010
Sample_last_update_date	Aug 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	Established from Dr. Shun-Yuan Jiang’s laboratory.
Sample_treatment_protocol_ch1	Inducible TIG1A, TIG1B, and control stable HCT116 clones were plated in 10-cm dishes overnight in growth medium, and then refreshed with medium containing 5 nM MFP for 24 h. Cells were washed twice with ice-cold PBS and harvested using cell lifter.
Sample_growth_protocol_ch1	culture medium: McCoy’s 5A medium supplemented with 25 mM HEPES, 26 mM NaHCO3, 2 mM L-glutamine, 100 units/ml penicillin, 100 micro g/ml streptomycin, 10% fetal bovine serum, 400 micro g/ml hygromycin and 125 micro g/ml zeocin.
Sample_growth_protocol_ch1	culture conduction: at 37ºC with 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using the RNeasy system (Qiagen, Valencia, CA, USA). The integrity of the total RNA was assessed using a 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA), and RNA integrity values reached more than 9.7 in all tested samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
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 Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with GeneChip® Operating Software v1.4 (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_data_processing	Gene expression data underwent secondary analysis using the GeneSpring GX program (Agilent Technologies, Santa Clara, CA, USA). Data were filtered based on both Detection Call and Signal Log Ratio in any of the comparisons between groups (control and TIG1A or control and TIG1B). Data declared “Absent” in all samples were filtered out. Samples had to be declared “Present” in at least two of three chips within a group to be maintained within the set. The log base 2.0 of the fold change was used as an additional filter. Filtered genes identified to be differentially expressed by 2-fold or greater in two of three chips were analyzed for functional gene clusters using GeneSpring. Statistical analyses were performed using one way ANOVA (p<0.05) and t-tests.
Sample_platform_id	GPL570
Sample_contact_name	Shun-Yuan,,Jiang
Sample_contact_department	Department of Research
Sample_contact_institute	Buddhist Tzu Chi General Hospital, Taipei Branch
Sample_contact_address	289 Jianguo Rd
Sample_contact_city	Sindian City
Sample_contact_state	Taipei county
Sample_contact_zip/postal_code	231
Sample_contact_country	Taiwan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587818/suppl/GSM587818.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587818/suppl/GSM587818.CHP.gz
Sample_series_id	GSE23882
Sample_data_row_count	54675

GSM587819

GPL570

Control_MFP_24hr_rep3

Control stable cells, mifepristone (5 nM) treatment, 24 hr.

cell line: colon cancer cell line HCT116 clone: Control stable clone agent: mifepristone dose: 5 nM time: 24 hr

Sample_geo_accession	GSM587819
Sample_status	Public on Aug 15 2011
Sample_submission_date	Aug 27 2010
Sample_last_update_date	Aug 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	Established from Dr. Shun-Yuan Jiang’s laboratory.
Sample_treatment_protocol_ch1	Inducible TIG1A, TIG1B, and control stable HCT116 clones were plated in 10-cm dishes overnight in growth medium, and then refreshed with medium containing 5 nM MFP for 24 h. Cells were washed twice with ice-cold PBS and harvested using cell lifter.
Sample_growth_protocol_ch1	culture medium: McCoy’s 5A medium supplemented with 25 mM HEPES, 26 mM NaHCO3, 2 mM L-glutamine, 100 units/ml penicillin, 100 micro g/ml streptomycin, 10% fetal bovine serum, 400 micro g/ml hygromycin and 125 micro g/ml zeocin.
Sample_growth_protocol_ch1	culture conduction: at 37ºC with 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using the RNeasy system (Qiagen, Valencia, CA, USA). The integrity of the total RNA was assessed using a 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA), and RNA integrity values reached more than 9.7 in all tested samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
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 Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with GeneChip® Operating Software v1.4 (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_data_processing	Gene expression data underwent secondary analysis using the GeneSpring GX program (Agilent Technologies, Santa Clara, CA, USA). Data were filtered based on both Detection Call and Signal Log Ratio in any of the comparisons between groups (control and TIG1A or control and TIG1B). Data declared “Absent” in all samples were filtered out. Samples had to be declared “Present” in at least two of three chips within a group to be maintained within the set. The log base 2.0 of the fold change was used as an additional filter. Filtered genes identified to be differentially expressed by 2-fold or greater in two of three chips were analyzed for functional gene clusters using GeneSpring. Statistical analyses were performed using one way ANOVA (p<0.05) and t-tests.
Sample_platform_id	GPL570
Sample_contact_name	Shun-Yuan,,Jiang
Sample_contact_department	Department of Research
Sample_contact_institute	Buddhist Tzu Chi General Hospital, Taipei Branch
Sample_contact_address	289 Jianguo Rd
Sample_contact_city	Sindian City
Sample_contact_state	Taipei county
Sample_contact_zip/postal_code	231
Sample_contact_country	Taiwan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587819/suppl/GSM587819.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587819/suppl/GSM587819.CHP.gz
Sample_series_id	GSE23882
Sample_data_row_count	54675

GSM587820

GPL570

TIG1A_MFP_24hr_rep1

TIG1A stable cells, mifepristone (5 nM) treatment, 24 hr.

cell line: colon cancer cell line HCT116 clone: TIG1A stable clone agent: mifepristone dose: 5 nM time: 24 hr

cells: Inducible TIG1A stable clone established from HCT116 colon cancer cells using the GeneSwitch system. stably integrated plasmids: pSwitch (Invitrogen, Carlsbad, CA, USA), inducible TIG1A expression plasmid (pTIG1A-V5). inducible protein: Recombinant TIG1A (RARRES1) isoform containing 294 amino acids of TIG1A fragment at the N-terminus and Myc and His tags at the C-terminus. inducer: mifepristone (5 nM), 24 hr

Sample_geo_accession	GSM587820
Sample_status	Public on Aug 15 2011
Sample_submission_date	Aug 27 2010
Sample_last_update_date	Aug 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	Established from Dr. Shun-Yuan Jiang’s laboratory.
Sample_treatment_protocol_ch1	Inducible TIG1A, TIG1B, and control stable HCT116 clones were plated in 10-cm dishes overnight in growth medium, and then refreshed with medium containing 5 nM MFP for 24 h. Cells were washed twice with ice-cold PBS and harvested using cell lifter.
Sample_growth_protocol_ch1	culture medium: McCoy’s 5A medium supplemented with 25 mM HEPES, 26 mM NaHCO3, 2 mM L-glutamine, 100 units/ml penicillin, 100 micro g/ml streptomycin, 10% fetal bovine serum, 400 micro g/ml hygromycin and 125 micro g/ml zeocin.
Sample_growth_protocol_ch1	culture conduction: at 37ºC with 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using the RNeasy system (Qiagen, Valencia, CA, USA). The integrity of the total RNA was assessed using a 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA), and RNA integrity values reached more than 9.7 in all tested samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
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 Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with GeneChip® Operating Software v1.4 (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_data_processing	Gene expression data underwent secondary analysis using the GeneSpring GX program (Agilent Technologies, Santa Clara, CA, USA). Data were filtered based on both Detection Call and Signal Log Ratio in any of the comparisons between groups (control and TIG1A or control and TIG1B). Data declared “Absent” in all samples were filtered out. Samples had to be declared “Present” in at least two of three chips within a group to be maintained within the set. The log base 2.0 of the fold change was used as an additional filter. Filtered genes identified to be differentially expressed by 2-fold or greater in two of three chips were analyzed for functional gene clusters using GeneSpring. Statistical analyses were performed using one way ANOVA (p<0.05) and t-tests.
Sample_platform_id	GPL570
Sample_contact_name	Shun-Yuan,,Jiang
Sample_contact_department	Department of Research
Sample_contact_institute	Buddhist Tzu Chi General Hospital, Taipei Branch
Sample_contact_address	289 Jianguo Rd
Sample_contact_city	Sindian City
Sample_contact_state	Taipei county
Sample_contact_zip/postal_code	231
Sample_contact_country	Taiwan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587820/suppl/GSM587820.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587820/suppl/GSM587820.CHP.gz
Sample_series_id	GSE23882
Sample_data_row_count	54675

GSM587821

GPL570

TIG1A_MFP_24hr_rep2

TIG1A stable cells, mifepristone (5 nM) treatment, 24 hr.

cell line: colon cancer cell line HCT116 clone: TIG1A stable clone agent: mifepristone dose: 5 nM time: 24 hr

Sample_geo_accession	GSM587821
Sample_status	Public on Aug 15 2011
Sample_submission_date	Aug 27 2010
Sample_last_update_date	Aug 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	Established from Dr. Shun-Yuan Jiang’s laboratory.
Sample_treatment_protocol_ch1	Inducible TIG1A, TIG1B, and control stable HCT116 clones were plated in 10-cm dishes overnight in growth medium, and then refreshed with medium containing 5 nM MFP for 24 h. Cells were washed twice with ice-cold PBS and harvested using cell lifter.
Sample_growth_protocol_ch1	culture medium: McCoy’s 5A medium supplemented with 25 mM HEPES, 26 mM NaHCO3, 2 mM L-glutamine, 100 units/ml penicillin, 100 micro g/ml streptomycin, 10% fetal bovine serum, 400 micro g/ml hygromycin and 125 micro g/ml zeocin.
Sample_growth_protocol_ch1	culture conduction: at 37ºC with 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using the RNeasy system (Qiagen, Valencia, CA, USA). The integrity of the total RNA was assessed using a 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA), and RNA integrity values reached more than 9.7 in all tested samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
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 Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with GeneChip® Operating Software v1.4 (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_data_processing	Gene expression data underwent secondary analysis using the GeneSpring GX program (Agilent Technologies, Santa Clara, CA, USA). Data were filtered based on both Detection Call and Signal Log Ratio in any of the comparisons between groups (control and TIG1A or control and TIG1B). Data declared “Absent” in all samples were filtered out. Samples had to be declared “Present” in at least two of three chips within a group to be maintained within the set. The log base 2.0 of the fold change was used as an additional filter. Filtered genes identified to be differentially expressed by 2-fold or greater in two of three chips were analyzed for functional gene clusters using GeneSpring. Statistical analyses were performed using one way ANOVA (p<0.05) and t-tests.
Sample_platform_id	GPL570
Sample_contact_name	Shun-Yuan,,Jiang
Sample_contact_department	Department of Research
Sample_contact_institute	Buddhist Tzu Chi General Hospital, Taipei Branch
Sample_contact_address	289 Jianguo Rd
Sample_contact_city	Sindian City
Sample_contact_state	Taipei county
Sample_contact_zip/postal_code	231
Sample_contact_country	Taiwan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587821/suppl/GSM587821.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587821/suppl/GSM587821.CHP.gz
Sample_series_id	GSE23882
Sample_data_row_count	54675

GSM587822

GPL570

TIG1A_MFP_24hr_rep3

TIG1A stable cells, mifepristone (5 nM) treatment, 24 hr.

cell line: colon cancer cell line HCT116 clone: TIG1A stable clone agent: mifepristone dose: 5 nM time: 24 hr

Sample_geo_accession	GSM587822
Sample_status	Public on Aug 15 2011
Sample_submission_date	Aug 27 2010
Sample_last_update_date	Aug 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	Established from Dr. Shun-Yuan Jiang’s laboratory.
Sample_treatment_protocol_ch1	Inducible TIG1A, TIG1B, and control stable HCT116 clones were plated in 10-cm dishes overnight in growth medium, and then refreshed with medium containing 5 nM MFP for 24 h. Cells were washed twice with ice-cold PBS and harvested using cell lifter.
Sample_growth_protocol_ch1	culture medium: McCoy’s 5A medium supplemented with 25 mM HEPES, 26 mM NaHCO3, 2 mM L-glutamine, 100 units/ml penicillin, 100 micro g/ml streptomycin, 10% fetal bovine serum, 400 micro g/ml hygromycin and 125 micro g/ml zeocin.
Sample_growth_protocol_ch1	culture conduction: at 37ºC with 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using the RNeasy system (Qiagen, Valencia, CA, USA). The integrity of the total RNA was assessed using a 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA), and RNA integrity values reached more than 9.7 in all tested samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
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 Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with GeneChip® Operating Software v1.4 (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_data_processing	Gene expression data underwent secondary analysis using the GeneSpring GX program (Agilent Technologies, Santa Clara, CA, USA). Data were filtered based on both Detection Call and Signal Log Ratio in any of the comparisons between groups (control and TIG1A or control and TIG1B). Data declared “Absent” in all samples were filtered out. Samples had to be declared “Present” in at least two of three chips within a group to be maintained within the set. The log base 2.0 of the fold change was used as an additional filter. Filtered genes identified to be differentially expressed by 2-fold or greater in two of three chips were analyzed for functional gene clusters using GeneSpring. Statistical analyses were performed using one way ANOVA (p<0.05) and t-tests.
Sample_platform_id	GPL570
Sample_contact_name	Shun-Yuan,,Jiang
Sample_contact_department	Department of Research
Sample_contact_institute	Buddhist Tzu Chi General Hospital, Taipei Branch
Sample_contact_address	289 Jianguo Rd
Sample_contact_city	Sindian City
Sample_contact_state	Taipei county
Sample_contact_zip/postal_code	231
Sample_contact_country	Taiwan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587822/suppl/GSM587822.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587822/suppl/GSM587822.CHP.gz
Sample_series_id	GSE23882
Sample_data_row_count	54675

GSM587823

GPL570

TIG1B_MFP_24hr_rep1

TIG1B stable cells, mifepristone (5 nM) treatment, 24 hr.

cell line: colon cancer cell line HCT116 clone: TIG1B stable clone agent: mifepristone dose: 5 nM time: 24 hr

cells: Inducible TIG1B stable clone established from HCT116 colon cancer cells using the GeneSwitch system. stably integrated plasmids: pSwitch (Invitrogen, Carlsbad, CA, USA), inducible TIG1B expression plasmid (pTIG1B-V5). inducible protein: Recombinant TIG1B (RARRES1) Isoform containing 228 amino acids of TIG1B fragment at the N-terminus and Myc and His tags at the C-terminus. inducer: mifepristone (5 nM), 24 hr

Sample_geo_accession	GSM587823
Sample_status	Public on Aug 15 2011
Sample_submission_date	Aug 27 2010
Sample_last_update_date	Aug 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	Established from Dr. Shun-Yuan Jiang’s laboratory.
Sample_treatment_protocol_ch1	Inducible TIG1A, TIG1B, and control stable HCT116 clones were plated in 10-cm dishes overnight in growth medium, and then refreshed with medium containing 5 nM MFP for 24 h. Cells were washed twice with ice-cold PBS and harvested using cell lifter.
Sample_growth_protocol_ch1	culture medium: McCoy’s 5A medium supplemented with 25 mM HEPES, 26 mM NaHCO3, 2 mM L-glutamine, 100 units/ml penicillin, 100 micro g/ml streptomycin, 10% fetal bovine serum, 400 micro g/ml hygromycin and 125 micro g/ml zeocin.
Sample_growth_protocol_ch1	culture conduction: at 37ºC with 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using the RNeasy system (Qiagen, Valencia, CA, USA). The integrity of the total RNA was assessed using a 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA), and RNA integrity values reached more than 9.7 in all tested samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
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 Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with GeneChip® Operating Software v1.4 (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_data_processing	Gene expression data underwent secondary analysis using the GeneSpring GX program (Agilent Technologies, Santa Clara, CA, USA). Data were filtered based on both Detection Call and Signal Log Ratio in any of the comparisons between groups (control and TIG1A or control and TIG1B). Data declared “Absent” in all samples were filtered out. Samples had to be declared “Present” in at least two of three chips within a group to be maintained within the set. The log base 2.0 of the fold change was used as an additional filter. Filtered genes identified to be differentially expressed by 2-fold or greater in two of three chips were analyzed for functional gene clusters using GeneSpring. Statistical analyses were performed using one way ANOVA (p<0.05) and t-tests.
Sample_platform_id	GPL570
Sample_contact_name	Shun-Yuan,,Jiang
Sample_contact_department	Department of Research
Sample_contact_institute	Buddhist Tzu Chi General Hospital, Taipei Branch
Sample_contact_address	289 Jianguo Rd
Sample_contact_city	Sindian City
Sample_contact_state	Taipei county
Sample_contact_zip/postal_code	231
Sample_contact_country	Taiwan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587823/suppl/GSM587823.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587823/suppl/GSM587823.CHP.gz
Sample_series_id	GSE23882
Sample_data_row_count	54675

GSM587824

GPL570

TIG1B_MFP_24hr_rep2

TIG1B stable cells, mifepristone (5 nM) treatment, 24 hr.

cell line: colon cancer cell line HCT116 clone: TIG1B stable clone agent: mifepristone dose: 5 nM time: 24 hr

Sample_geo_accession	GSM587824
Sample_status	Public on Aug 15 2011
Sample_submission_date	Aug 27 2010
Sample_last_update_date	Aug 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	Established from Dr. Shun-Yuan Jiang’s laboratory.
Sample_treatment_protocol_ch1	Inducible TIG1A, TIG1B, and control stable HCT116 clones were plated in 10-cm dishes overnight in growth medium, and then refreshed with medium containing 5 nM MFP for 24 h. Cells were washed twice with ice-cold PBS and harvested using cell lifter.
Sample_growth_protocol_ch1	culture medium: McCoy’s 5A medium supplemented with 25 mM HEPES, 26 mM NaHCO3, 2 mM L-glutamine, 100 units/ml penicillin, 100 micro g/ml streptomycin, 10% fetal bovine serum, 400 micro g/ml hygromycin and 125 micro g/ml zeocin.
Sample_growth_protocol_ch1	culture conduction: at 37ºC with 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using the RNeasy system (Qiagen, Valencia, CA, USA). The integrity of the total RNA was assessed using a 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA), and RNA integrity values reached more than 9.7 in all tested samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
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 Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with GeneChip® Operating Software v1.4 (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_data_processing	Gene expression data underwent secondary analysis using the GeneSpring GX program (Agilent Technologies, Santa Clara, CA, USA). Data were filtered based on both Detection Call and Signal Log Ratio in any of the comparisons between groups (control and TIG1A or control and TIG1B). Data declared “Absent” in all samples were filtered out. Samples had to be declared “Present” in at least two of three chips within a group to be maintained within the set. The log base 2.0 of the fold change was used as an additional filter. Filtered genes identified to be differentially expressed by 2-fold or greater in two of three chips were analyzed for functional gene clusters using GeneSpring. Statistical analyses were performed using one way ANOVA (p<0.05) and t-tests.
Sample_platform_id	GPL570
Sample_contact_name	Shun-Yuan,,Jiang
Sample_contact_department	Department of Research
Sample_contact_institute	Buddhist Tzu Chi General Hospital, Taipei Branch
Sample_contact_address	289 Jianguo Rd
Sample_contact_city	Sindian City
Sample_contact_state	Taipei county
Sample_contact_zip/postal_code	231
Sample_contact_country	Taiwan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587824/suppl/GSM587824.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587824/suppl/GSM587824.CHP.gz
Sample_series_id	GSE23882
Sample_data_row_count	54675

GSM587825

GPL570

TIG1B_MFP_24hr_rep3

TIG1B stable cells, mifepristone (5 nM) treatment, 24 hr.

cell line: colon cancer cell line HCT116 clone: TIG1B stable clone agent: mifepristone dose: 5 nM time: 24 hr

Sample_geo_accession	GSM587825
Sample_status	Public on Aug 15 2011
Sample_submission_date	Aug 27 2010
Sample_last_update_date	Aug 15 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	Established from Dr. Shun-Yuan Jiang’s laboratory.
Sample_treatment_protocol_ch1	Inducible TIG1A, TIG1B, and control stable HCT116 clones were plated in 10-cm dishes overnight in growth medium, and then refreshed with medium containing 5 nM MFP for 24 h. Cells were washed twice with ice-cold PBS and harvested using cell lifter.
Sample_growth_protocol_ch1	culture medium: McCoy’s 5A medium supplemented with 25 mM HEPES, 26 mM NaHCO3, 2 mM L-glutamine, 100 units/ml penicillin, 100 micro g/ml streptomycin, 10% fetal bovine serum, 400 micro g/ml hygromycin and 125 micro g/ml zeocin.
Sample_growth_protocol_ch1	culture conduction: at 37ºC with 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using the RNeasy system (Qiagen, Valencia, CA, USA). The integrity of the total RNA was assessed using a 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA), and RNA integrity values reached more than 9.7 in all tested samples.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.
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 Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with GeneChip® Operating Software v1.4 (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_data_processing	Gene expression data underwent secondary analysis using the GeneSpring GX program (Agilent Technologies, Santa Clara, CA, USA). Data were filtered based on both Detection Call and Signal Log Ratio in any of the comparisons between groups (control and TIG1A or control and TIG1B). Data declared “Absent” in all samples were filtered out. Samples had to be declared “Present” in at least two of three chips within a group to be maintained within the set. The log base 2.0 of the fold change was used as an additional filter. Filtered genes identified to be differentially expressed by 2-fold or greater in two of three chips were analyzed for functional gene clusters using GeneSpring. Statistical analyses were performed using one way ANOVA (p<0.05) and t-tests.
Sample_platform_id	GPL570
Sample_contact_name	Shun-Yuan,,Jiang
Sample_contact_department	Department of Research
Sample_contact_institute	Buddhist Tzu Chi General Hospital, Taipei Branch
Sample_contact_address	289 Jianguo Rd
Sample_contact_city	Sindian City
Sample_contact_state	Taipei county
Sample_contact_zip/postal_code	231
Sample_contact_country	Taiwan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587825/suppl/GSM587825.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM587nnn/GSM587825/suppl/GSM587825.CHP.gz
Sample_series_id	GSE23882
Sample_data_row_count	54675

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