Search results for the GEO ID: GSE16416  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM412619 | GPL570 |
|
Cells treated with medium as control, biological rep 1
|
Cells treated with medium as control
|
tissue: Human foreskin fibroblasts (HFF) BJ
|
Gene expression data from untreated human fibroblast
|
| Sample_geo_accession | GSM412619
| | Sample_status | Public on Sep 09 2011
| | Sample_submission_date | Jun 03 2009
| | Sample_last_update_date | Sep 09 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Culture cells were stimulated with 5 ng/ml TGF-β1 for 3 hours in the presence or absence of T. cruzi conditioned medium.
| | Sample_growth_protocol_ch1 | 5X10^4/ml cells were seeded in in 75 mm culture plates in Dulbecco's modified Eagle medium (10%FBS,100 U/ml penicillin, 100 ug/ml streptomycin, 2mM glutamine) and allowed to grow for 48 hours at 37 C in a CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by concentration using the RNeasy kit (Quiagen).
| | 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, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG_U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data was uploaded into the Rosetta Resolver System for data processing and normalization using the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). The expression profiles from replicate samples were combined into ratio experiments. Each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference. Sequences with absolute fold-change >=2 and p-value <= 0.01 were considered as differentially expressed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jaime ,Alfredo,Costales
| | Sample_contact_email | jacostalesc@puce.edu.ec, jaimecostales@gmail.com
| | Sample_contact_laboratory | Center for Infectious Disease Research
| | Sample_contact_department | Biological Sciences
| | Sample_contact_institute | Pontificia Universidad Catolica del Ecuador
| | Sample_contact_address | 12 de Octubre y Patria
| | Sample_contact_city | Quito
| | Sample_contact_zip/postal_code | NN
| | Sample_contact_country | Ecuador
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412619/suppl/GSM412619.CEL.gz
| | Sample_series_id | GSE16416
| | Sample_data_row_count | 54675
| | |
|
GSM412620 | GPL570 |
|
Cells treated with medium as control, biological rep 2
|
Cells treated with medium as control
|
tissue: Human foreskin fibroblasts (HFF) BJ
|
Gene expression data from untreated human fibroblast
|
| Sample_geo_accession | GSM412620
| | Sample_status | Public on Sep 09 2011
| | Sample_submission_date | Jun 03 2009
| | Sample_last_update_date | Sep 09 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Culture cells were stimulated with 5 ng/ml TGF-β1 for 3 hours in the presence or absence of T. cruzi conditioned medium.
| | Sample_growth_protocol_ch1 | 5X10^4/ml cells were seeded in in 75 mm culture plates in Dulbecco's modified Eagle medium (10%FBS,100 U/ml penicillin, 100 ug/ml streptomycin, 2mM glutamine) and allowed to grow for 48 hours at 37 C in a CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by concentration using the RNeasy kit (Quiagen).
| | 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, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG_U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data was uploaded into the Rosetta Resolver System for data processing and normalization using the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). The expression profiles from replicate samples were combined into ratio experiments. Each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference. Sequences with absolute fold-change >=2 and p-value <= 0.01 were considered as differentially expressed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jaime ,Alfredo,Costales
| | Sample_contact_email | jacostalesc@puce.edu.ec, jaimecostales@gmail.com
| | Sample_contact_laboratory | Center for Infectious Disease Research
| | Sample_contact_department | Biological Sciences
| | Sample_contact_institute | Pontificia Universidad Catolica del Ecuador
| | Sample_contact_address | 12 de Octubre y Patria
| | Sample_contact_city | Quito
| | Sample_contact_zip/postal_code | NN
| | Sample_contact_country | Ecuador
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412620/suppl/GSM412620.CEL.gz
| | Sample_series_id | GSE16416
| | Sample_data_row_count | 54675
| | |
|
GSM412621 | GPL570 |
|
Cells treated with medium as control, biological rep 3
|
Cells treated with medium as control
|
tissue: Human foreskin fibroblasts (HFF) BJ
|
Gene expression data from untreated human fibroblast
|
| Sample_geo_accession | GSM412621
| | Sample_status | Public on Sep 09 2011
| | Sample_submission_date | Jun 03 2009
| | Sample_last_update_date | Sep 09 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Culture cells were stimulated with 5 ng/ml TGF-β1 for 3 hours in the presence or absence of T. cruzi conditioned medium.
| | Sample_growth_protocol_ch1 | 5X10^4/ml cells were seeded in in 75 mm culture plates in Dulbecco's modified Eagle medium (10%FBS,100 U/ml penicillin, 100 ug/ml streptomycin, 2mM glutamine) and allowed to grow for 48 hours at 37 C in a CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by concentration using the RNeasy kit (Quiagen).
| | 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, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG_U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data was uploaded into the Rosetta Resolver System for data processing and normalization using the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). The expression profiles from replicate samples were combined into ratio experiments. Each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference. Sequences with absolute fold-change >=2 and p-value <= 0.01 were considered as differentially expressed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jaime ,Alfredo,Costales
| | Sample_contact_email | jacostalesc@puce.edu.ec, jaimecostales@gmail.com
| | Sample_contact_laboratory | Center for Infectious Disease Research
| | Sample_contact_department | Biological Sciences
| | Sample_contact_institute | Pontificia Universidad Catolica del Ecuador
| | Sample_contact_address | 12 de Octubre y Patria
| | Sample_contact_city | Quito
| | Sample_contact_zip/postal_code | NN
| | Sample_contact_country | Ecuador
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412621/suppl/GSM412621.CEL.gz
| | Sample_series_id | GSE16416
| | Sample_data_row_count | 54675
| | |
|
GSM412622 | GPL570 |
|
Cells treated with parasite conditioned medium, biological rep 1
|
Cells treated with parasite conditioned medium
|
tissue: Human foreskin fibroblasts (HFF) BJ
|
Gene expression data from human fibroblast treated with Trypanosoma cruzi conditioned medium
|
| Sample_geo_accession | GSM412622
| | Sample_status | Public on Sep 09 2011
| | Sample_submission_date | Jun 03 2009
| | Sample_last_update_date | Sep 09 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Culture cells were stimulated with 5 ng/ml TGF-β1 for 3 hours in the presence or absence of T. cruzi conditioned medium.
| | Sample_growth_protocol_ch1 | 5X10^4/ml cells were seeded in in 75 mm culture plates in Dulbecco's modified Eagle medium (10%FBS,100 U/ml penicillin, 100 ug/ml streptomycin, 2mM glutamine) and allowed to grow for 48 hours at 37 C in a CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by concentration using the RNeasy kit (Quiagen).
| | 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, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG_U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data was uploaded into the Rosetta Resolver System for data processing and normalization using the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). The expression profiles from replicate samples were combined into ratio experiments. Each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference. Sequences with absolute fold-change >=2 and p-value <= 0.01 were considered as differentially expressed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jaime ,Alfredo,Costales
| | Sample_contact_email | jacostalesc@puce.edu.ec, jaimecostales@gmail.com
| | Sample_contact_laboratory | Center for Infectious Disease Research
| | Sample_contact_department | Biological Sciences
| | Sample_contact_institute | Pontificia Universidad Catolica del Ecuador
| | Sample_contact_address | 12 de Octubre y Patria
| | Sample_contact_city | Quito
| | Sample_contact_zip/postal_code | NN
| | Sample_contact_country | Ecuador
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412622/suppl/GSM412622.CEL.gz
| | Sample_series_id | GSE16416
| | Sample_data_row_count | 54675
| | |
|
GSM412623 | GPL570 |
|
Cells treated with parasite conditioned medium, biological rep 2
|
Cells treated with parasite conditioned medium
|
tissue: Human foreskin fibroblasts (HFF) BJ
|
Gene expression data from human fibroblast treated with Trypanosoma cruzi conditioned medium
|
| Sample_geo_accession | GSM412623
| | Sample_status | Public on Sep 09 2011
| | Sample_submission_date | Jun 03 2009
| | Sample_last_update_date | Sep 09 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Culture cells were stimulated with 5 ng/ml TGF-β1 for 3 hours in the presence or absence of T. cruzi conditioned medium.
| | Sample_growth_protocol_ch1 | 5X10^4/ml cells were seeded in in 75 mm culture plates in Dulbecco's modified Eagle medium (10%FBS,100 U/ml penicillin, 100 ug/ml streptomycin, 2mM glutamine) and allowed to grow for 48 hours at 37 C in a CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by concentration using the RNeasy kit (Quiagen).
| | 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, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG_U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data was uploaded into the Rosetta Resolver System for data processing and normalization using the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). The expression profiles from replicate samples were combined into ratio experiments. Each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference. Sequences with absolute fold-change >=2 and p-value <= 0.01 were considered as differentially expressed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jaime ,Alfredo,Costales
| | Sample_contact_email | jacostalesc@puce.edu.ec, jaimecostales@gmail.com
| | Sample_contact_laboratory | Center for Infectious Disease Research
| | Sample_contact_department | Biological Sciences
| | Sample_contact_institute | Pontificia Universidad Catolica del Ecuador
| | Sample_contact_address | 12 de Octubre y Patria
| | Sample_contact_city | Quito
| | Sample_contact_zip/postal_code | NN
| | Sample_contact_country | Ecuador
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412623/suppl/GSM412623.CEL.gz
| | Sample_series_id | GSE16416
| | Sample_data_row_count | 54675
| | |
|
GSM412624 | GPL570 |
|
Cells treated with parasite conditioned medium, biological rep 3
|
Cells treated with parasite conditioned medium
|
tissue: Human foreskin fibroblasts (HFF) BJ
|
Gene expression data from human fibroblast treated with Trypanosoma cruzi conditioned medium
|
| Sample_geo_accession | GSM412624
| | Sample_status | Public on Sep 09 2011
| | Sample_submission_date | Jun 03 2009
| | Sample_last_update_date | Sep 09 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Culture cells were stimulated with 5 ng/ml TGF-β1 for 3 hours in the presence or absence of T. cruzi conditioned medium.
| | Sample_growth_protocol_ch1 | 5X10^4/ml cells were seeded in in 75 mm culture plates in Dulbecco's modified Eagle medium (10%FBS,100 U/ml penicillin, 100 ug/ml streptomycin, 2mM glutamine) and allowed to grow for 48 hours at 37 C in a CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by concentration using the RNeasy kit (Quiagen).
| | 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, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG_U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data was uploaded into the Rosetta Resolver System for data processing and normalization using the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). The expression profiles from replicate samples were combined into ratio experiments. Each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference. Sequences with absolute fold-change >=2 and p-value <= 0.01 were considered as differentially expressed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jaime ,Alfredo,Costales
| | Sample_contact_email | jacostalesc@puce.edu.ec, jaimecostales@gmail.com
| | Sample_contact_laboratory | Center for Infectious Disease Research
| | Sample_contact_department | Biological Sciences
| | Sample_contact_institute | Pontificia Universidad Catolica del Ecuador
| | Sample_contact_address | 12 de Octubre y Patria
| | Sample_contact_city | Quito
| | Sample_contact_zip/postal_code | NN
| | Sample_contact_country | Ecuador
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412624/suppl/GSM412624.CEL.gz
| | Sample_series_id | GSE16416
| | Sample_data_row_count | 54675
| | |
|
GSM412625 | GPL570 |
|
Cells treated with TGF, biological rep 1
|
Cells treated with TGF
|
tissue: Human foreskin fibroblasts (HFF) BJ
|
Gene expression data from human fibroblast treated with TGF as positive control for fibrotic gene activation
|
| Sample_geo_accession | GSM412625
| | Sample_status | Public on Sep 09 2011
| | Sample_submission_date | Jun 03 2009
| | Sample_last_update_date | Sep 09 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Culture cells were stimulated with 5 ng/ml TGF-β1 for 3 hours in the presence or absence of T. cruzi conditioned medium.
| | Sample_growth_protocol_ch1 | 5X10^4/ml cells were seeded in in 75 mm culture plates in Dulbecco's modified Eagle medium (10%FBS,100 U/ml penicillin, 100 ug/ml streptomycin, 2mM glutamine) and allowed to grow for 48 hours at 37 C in a CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by concentration using the RNeasy kit (Quiagen).
| | 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, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG_U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data was uploaded into the Rosetta Resolver System for data processing and normalization using the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). The expression profiles from replicate samples were combined into ratio experiments. Each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference. Sequences with absolute fold-change >=2 and p-value <= 0.01 were considered as differentially expressed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jaime ,Alfredo,Costales
| | Sample_contact_email | jacostalesc@puce.edu.ec, jaimecostales@gmail.com
| | Sample_contact_laboratory | Center for Infectious Disease Research
| | Sample_contact_department | Biological Sciences
| | Sample_contact_institute | Pontificia Universidad Catolica del Ecuador
| | Sample_contact_address | 12 de Octubre y Patria
| | Sample_contact_city | Quito
| | Sample_contact_zip/postal_code | NN
| | Sample_contact_country | Ecuador
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412625/suppl/GSM412625.CEL.gz
| | Sample_series_id | GSE16416
| | Sample_data_row_count | 54675
| | |
|
GSM412626 | GPL570 |
|
Cells treated with TGF, biological rep 2
|
Cells treated with TGF
|
tissue: Human foreskin fibroblasts (HFF) BJ
|
Gene expression data from human fibroblast treated with TGF as positive control for fibrotic gene activation
|
| Sample_geo_accession | GSM412626
| | Sample_status | Public on Sep 09 2011
| | Sample_submission_date | Jun 03 2009
| | Sample_last_update_date | Sep 09 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Culture cells were stimulated with 5 ng/ml TGF-β1 for 3 hours in the presence or absence of T. cruzi conditioned medium.
| | Sample_growth_protocol_ch1 | 5X10^4/ml cells were seeded in in 75 mm culture plates in Dulbecco's modified Eagle medium (10%FBS,100 U/ml penicillin, 100 ug/ml streptomycin, 2mM glutamine) and allowed to grow for 48 hours at 37 C in a CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by concentration using the RNeasy kit (Quiagen).
| | 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, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG_U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data was uploaded into the Rosetta Resolver System for data processing and normalization using the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). The expression profiles from replicate samples were combined into ratio experiments. Each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference. Sequences with absolute fold-change >=2 and p-value <= 0.01 were considered as differentially expressed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jaime ,Alfredo,Costales
| | Sample_contact_email | jacostalesc@puce.edu.ec, jaimecostales@gmail.com
| | Sample_contact_laboratory | Center for Infectious Disease Research
| | Sample_contact_department | Biological Sciences
| | Sample_contact_institute | Pontificia Universidad Catolica del Ecuador
| | Sample_contact_address | 12 de Octubre y Patria
| | Sample_contact_city | Quito
| | Sample_contact_zip/postal_code | NN
| | Sample_contact_country | Ecuador
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412626/suppl/GSM412626.CEL.gz
| | Sample_series_id | GSE16416
| | Sample_data_row_count | 54675
| | |
|
GSM412627 | GPL570 |
|
Cells treated with TGF, biological rep 3
|
Cells treated with TGF
|
tissue: Human foreskin fibroblasts (HFF) BJ
|
Gene expression data from human fibroblast treated with TGF as positive control for fibrotic gene activation
|
| Sample_geo_accession | GSM412627
| | Sample_status | Public on Sep 09 2011
| | Sample_submission_date | Jun 03 2009
| | Sample_last_update_date | Sep 09 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Culture cells were stimulated with 5 ng/ml TGF-β1 for 3 hours in the presence or absence of T. cruzi conditioned medium.
| | Sample_growth_protocol_ch1 | 5X10^4/ml cells were seeded in in 75 mm culture plates in Dulbecco's modified Eagle medium (10%FBS,100 U/ml penicillin, 100 ug/ml streptomycin, 2mM glutamine) and allowed to grow for 48 hours at 37 C in a CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by concentration using the RNeasy kit (Quiagen).
| | 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, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG_U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data was uploaded into the Rosetta Resolver System for data processing and normalization using the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). The expression profiles from replicate samples were combined into ratio experiments. Each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference. Sequences with absolute fold-change >=2 and p-value <= 0.01 were considered as differentially expressed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jaime ,Alfredo,Costales
| | Sample_contact_email | jacostalesc@puce.edu.ec, jaimecostales@gmail.com
| | Sample_contact_laboratory | Center for Infectious Disease Research
| | Sample_contact_department | Biological Sciences
| | Sample_contact_institute | Pontificia Universidad Catolica del Ecuador
| | Sample_contact_address | 12 de Octubre y Patria
| | Sample_contact_city | Quito
| | Sample_contact_zip/postal_code | NN
| | Sample_contact_country | Ecuador
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412627/suppl/GSM412627.CEL.gz
| | Sample_series_id | GSE16416
| | Sample_data_row_count | 54675
| | |
|
GSM412628 | GPL570 |
|
Cells treated with TGF and parasite conditioned medium, biological rep 1
|
Cells treated with TGF and parasite conditioned medium
|
tissue: Human foreskin fibroblasts (HFF) BJ
|
Gene expression data from human fibroblast treated simultaneously with TGF and Trypanosoma cruzi conditioned medium to measure abrogation of fibrotic gene activation
|
| Sample_geo_accession | GSM412628
| | Sample_status | Public on Sep 09 2011
| | Sample_submission_date | Jun 03 2009
| | Sample_last_update_date | Sep 09 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Culture cells were stimulated with 5 ng/ml TGF-β1 for 3 hours in the presence or absence of T. cruzi conditioned medium.
| | Sample_growth_protocol_ch1 | 5X10^4/ml cells were seeded in in 75 mm culture plates in Dulbecco's modified Eagle medium (10%FBS,100 U/ml penicillin, 100 ug/ml streptomycin, 2mM glutamine) and allowed to grow for 48 hours at 37 C in a CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by concentration using the RNeasy kit (Quiagen).
| | 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, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG_U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data was uploaded into the Rosetta Resolver System for data processing and normalization using the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). The expression profiles from replicate samples were combined into ratio experiments. Each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference. Sequences with absolute fold-change >=2 and p-value <= 0.01 were considered as differentially expressed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jaime ,Alfredo,Costales
| | Sample_contact_email | jacostalesc@puce.edu.ec, jaimecostales@gmail.com
| | Sample_contact_laboratory | Center for Infectious Disease Research
| | Sample_contact_department | Biological Sciences
| | Sample_contact_institute | Pontificia Universidad Catolica del Ecuador
| | Sample_contact_address | 12 de Octubre y Patria
| | Sample_contact_city | Quito
| | Sample_contact_zip/postal_code | NN
| | Sample_contact_country | Ecuador
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412628/suppl/GSM412628.CEL.gz
| | Sample_series_id | GSE16416
| | Sample_data_row_count | 54675
| | |
|
GSM412629 | GPL570 |
|
Cells treated with TGF and parasite conditioned medium, biological rep 2
|
Cells treated with TGF and parasite conditioned medium
|
tissue: Human foreskin fibroblasts (HFF) BJ
|
Gene expression data from human fibroblast treated simultaneously with TGF and Trypanosoma cruzi conditioned medium to measure abrogation of fibrotic gene activation
|
| Sample_geo_accession | GSM412629
| | Sample_status | Public on Sep 09 2011
| | Sample_submission_date | Jun 03 2009
| | Sample_last_update_date | Sep 09 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Culture cells were stimulated with 5 ng/ml TGF-β1 for 3 hours in the presence or absence of T. cruzi conditioned medium.
| | Sample_growth_protocol_ch1 | 5X10^4/ml cells were seeded in in 75 mm culture plates in Dulbecco's modified Eagle medium (10%FBS,100 U/ml penicillin, 100 ug/ml streptomycin, 2mM glutamine) and allowed to grow for 48 hours at 37 C in a CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by concentration using the RNeasy kit (Quiagen).
| | 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, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG_U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data was uploaded into the Rosetta Resolver System for data processing and normalization using the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). The expression profiles from replicate samples were combined into ratio experiments. Each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference. Sequences with absolute fold-change >=2 and p-value <= 0.01 were considered as differentially expressed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jaime ,Alfredo,Costales
| | Sample_contact_email | jacostalesc@puce.edu.ec, jaimecostales@gmail.com
| | Sample_contact_laboratory | Center for Infectious Disease Research
| | Sample_contact_department | Biological Sciences
| | Sample_contact_institute | Pontificia Universidad Catolica del Ecuador
| | Sample_contact_address | 12 de Octubre y Patria
| | Sample_contact_city | Quito
| | Sample_contact_zip/postal_code | NN
| | Sample_contact_country | Ecuador
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412629/suppl/GSM412629.CEL.gz
| | Sample_series_id | GSE16416
| | Sample_data_row_count | 54675
| | |
|
GSM412630 | GPL570 |
|
Cells treated with TGF and parasite conditioned medium, biological rep 3
|
Cells treated with TGF and parasite conditioned medium
|
tissue: Human foreskin fibroblasts (HFF) BJ
|
Gene expression data from human fibroblast treated simultaneously with TGF and Trypanosoma cruzi conditioned medium to measure abrogation of fibrotic gene activation
|
| Sample_geo_accession | GSM412630
| | Sample_status | Public on Sep 09 2011
| | Sample_submission_date | Jun 03 2009
| | Sample_last_update_date | Sep 09 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Culture cells were stimulated with 5 ng/ml TGF-β1 for 3 hours in the presence or absence of T. cruzi conditioned medium.
| | Sample_growth_protocol_ch1 | 5X10^4/ml cells were seeded in in 75 mm culture plates in Dulbecco's modified Eagle medium (10%FBS,100 U/ml penicillin, 100 ug/ml streptomycin, 2mM glutamine) and allowed to grow for 48 hours at 37 C in a CO2 incubator
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by concentration using the RNeasy kit (Quiagen).
| | 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, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG_U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | The raw data was uploaded into the Rosetta Resolver System for data processing and normalization using the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). The expression profiles from replicate samples were combined into ratio experiments. Each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference. Sequences with absolute fold-change >=2 and p-value <= 0.01 were considered as differentially expressed.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Jaime ,Alfredo,Costales
| | Sample_contact_email | jacostalesc@puce.edu.ec, jaimecostales@gmail.com
| | Sample_contact_laboratory | Center for Infectious Disease Research
| | Sample_contact_department | Biological Sciences
| | Sample_contact_institute | Pontificia Universidad Catolica del Ecuador
| | Sample_contact_address | 12 de Octubre y Patria
| | Sample_contact_city | Quito
| | Sample_contact_zip/postal_code | NN
| | Sample_contact_country | Ecuador
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM412nnn/GSM412630/suppl/GSM412630.CEL.gz
| | Sample_series_id | GSE16416
| | Sample_data_row_count | 54675
| | |
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