Search results for the GEO ID: GSE39293  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM960275 | GPL570 |
|
1-HeLa control a
|
HeLa cells, 72h growth
|
organ: cervix
disease: adenocarcinoma
cell type: epithelial
cell line: HeLa
|
---
|
| Sample_geo_accession | GSM960275
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC: CCL-2™
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960275/suppl/GSM960275_hyb12843.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960276 | GPL570 |
|
4-HeLa HPMPC a
|
HeLa cells, 72h growth + 50µg/ml cidofovir
|
organ: cervix
disease: adenocarcinoma
cell type: epithelial
cell line: HeLa
|
---
|
| Sample_geo_accession | GSM960276
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC: CCL-2™
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium + 50 µg/ml cidofovir
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960276/suppl/GSM960276_hyb12844.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960277 | GPL570 |
|
7-HeLa 52 a
|
HeLa cells cidofovir resistant (#52), 72h growth
|
organ: cervix
disease: adenocarcinoma
cell type: epithelial
cell line: HeLa
|
---
|
| Sample_geo_accession | GSM960277
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC: CCL-2™
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960277/suppl/GSM960277_hyb12845.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960278 | GPL570 |
|
10-HaCaT control a
|
HaCaT cells, 72h growth
|
tissue: skin
cell type: keratinocyte
description: in vitro spontaneously transformed
cell line: HaCaT
|
---
|
| Sample_geo_accession | GSM960278
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | CLS: #300493
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960278/suppl/GSM960278_hyb12846.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960279 | GPL570 |
|
13-HaCaT HPMPC a
|
HaCaT cells, 72h growth + 50µg/ml cidofovir
|
tissue: skin
cell type: keratinocyte
description: in vitro spontaneously transformed
cell line: HaCaT
|
---
|
| Sample_geo_accession | GSM960279
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | CLS: #300493
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium + 50 µg/ml cidofovir
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960279/suppl/GSM960279_hyb12847.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960280 | GPL570 |
|
16-HaCaT 51 a
|
HaCaT cells cidofovir resistant (#51), 72h growth
|
tissue: skin
cell type: keratinocyte
description: in vitro spontaneously transformed
cell line: HaCaT
|
---
|
| Sample_geo_accession | GSM960280
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | CLS: #300493
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960280/suppl/GSM960280_hyb12848.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960281 | GPL570 |
|
19-PHK control a
|
PHK cells, 72h growth
|
cell type: primary human keratinocytes
tissue: neonatal foreskin
|
---
|
| Sample_geo_accession | GSM960281
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | patient sample
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in Keratinocyte Serum Free medium
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960281/suppl/GSM960281_hyb12849.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960282 | GPL570 |
|
22-PHK HPMPC a
|
PHK cells, 72h growth + 50µg/ml cidofovir
|
cell type: primary human keratinocytes
tissue: neonatal foreskin
|
---
|
| Sample_geo_accession | GSM960282
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | patient sample
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium + 50 µg/ml cidofovir
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in Keratinocyte Serum Free medium
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960282/suppl/GSM960282_hyb12850.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960283 | GPL570 |
|
2-HeLa control b
|
HeLa cells, 72h growth
|
organ: cervix
disease: adenocarcinoma
cell type: epithelial
cell line: HeLa
|
---
|
| Sample_geo_accession | GSM960283
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC: CCL-2™
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960283/suppl/GSM960283_hyb12851.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960284 | GPL570 |
|
5-HeLa HPMPC b
|
HeLa cells, 72h growth + 50µg/ml cidofovir
|
organ: cervix
disease: adenocarcinoma
cell type: epithelial
cell line: HeLa
|
---
|
| Sample_geo_accession | GSM960284
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC: CCL-2™
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium + 50 µg/ml cidofovir
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960284/suppl/GSM960284_hyb12852.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960285 | GPL570 |
|
8-HeLa 52 b
|
HeLa cells cidofovir resistant (#52), 72h growth
|
organ: cervix
disease: adenocarcinoma
cell type: epithelial
cell line: HeLa
|
---
|
| Sample_geo_accession | GSM960285
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC: CCL-2™
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960285/suppl/GSM960285_hyb12853.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960286 | GPL570 |
|
11-HaCaT control b
|
HaCaT cells, 72h growth
|
tissue: skin
cell type: keratinocyte
description: in vitro spontaneously transformed
cell line: HaCaT
|
---
|
| Sample_geo_accession | GSM960286
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | CLS: #300493
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960286/suppl/GSM960286_hyb12854.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960287 | GPL570 |
|
14-HaCaT HPMPC b
|
HaCaT cells, 72h growth + 50µg/ml cidofovir
|
tissue: skin
cell type: keratinocyte
description: in vitro spontaneously transformed
cell line: HaCaT
|
---
|
| Sample_geo_accession | GSM960287
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | CLS: #300493
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium + 50 µg/ml cidofovir
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960287/suppl/GSM960287_hyb12855.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960288 | GPL570 |
|
17-HaCaT 51
|
HaCaT cells cidofovir resistant (#51), 72h growth
|
tissue: skin
cell type: keratinocyte
description: in vitro spontaneously transformed
cell line: HaCaT
|
---
|
| Sample_geo_accession | GSM960288
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | CLS: #300493
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960288/suppl/GSM960288_hyb12856.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960289 | GPL570 |
|
20-PHK control b
|
PHK cells, 72h growth
|
cell type: primary human keratinocytes
tissue: neonatal foreskin
|
---
|
| Sample_geo_accession | GSM960289
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | patient sample
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in Keratinocyte Serum Free medium
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960289/suppl/GSM960289_hyb12857.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960290 | GPL570 |
|
23-PHK HPMPC b
|
PHK cells, 72h growth + 50µg/ml cidofovir
|
cell type: primary human keratinocytes
tissue: neonatal foreskin
|
---
|
| Sample_geo_accession | GSM960290
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | patient sample
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium + 50 µg/ml cidofovir
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in Keratinocyte Serum Free medium
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960290/suppl/GSM960290_hyb12858.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960291 | GPL570 |
|
3-HeLa control c
|
HeLa cells, 72h growth
|
organ: cervix
disease: adenocarcinoma
cell type: epithelial
cell line: HeLa
|
---
|
| Sample_geo_accession | GSM960291
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC: CCL-2™
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960291/suppl/GSM960291_hyb12859.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960292 | GPL570 |
|
6-HeLa HPMPC c
|
HeLa cells, 72h growth + 50µg/ml cidofovir
|
organ: cervix
disease: adenocarcinoma
cell type: epithelial
cell line: HeLa
|
---
|
| Sample_geo_accession | GSM960292
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC: CCL-2™
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium + 50 µg/ml cidofovir
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960292/suppl/GSM960292_hyb12860.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960293 | GPL570 |
|
9-HeLa 52 c
|
HeLa cells cidofovir resistant (#52), 72h growth
|
organ: cervix
disease: adenocarcinoma
cell type: epithelial
cell line: HeLa
|
---
|
| Sample_geo_accession | GSM960293
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC: CCL-2™
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960293/suppl/GSM960293_hyb12861.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960294 | GPL570 |
|
12-HaCaT control c
|
HaCaT cells, 72h growth
|
tissue: skin
cell type: keratinocyte
description: in vitro spontaneously transformed
cell line: HaCaT
|
---
|
| Sample_geo_accession | GSM960294
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | CLS: #300493
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960294/suppl/GSM960294_hyb12862.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960295 | GPL570 |
|
15-HaCaT HPMPC c
|
HaCaT cells, 72h growth + 50µg/ml cidofovir
|
tissue: skin
cell type: keratinocyte
description: in vitro spontaneously transformed
cell line: HaCaT
|
---
|
| Sample_geo_accession | GSM960295
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | CLS: #300493
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium + 50 µg/ml cidofovir
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960295/suppl/GSM960295_hyb12863.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960296 | GPL570 |
|
18-HaCaT 51 c
|
HaCaT cells cidofovir resistant (#51), 72h growth
|
tissue: skin
cell type: keratinocyte
description: in vitro spontaneously transformed
cell line: HaCaT
|
---
|
| Sample_geo_accession | GSM960296
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | CLS: #300493
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960296/suppl/GSM960296_hyb12864.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960297 | GPL570 |
|
21-PHK control c
|
PHK cells, 72h growth
|
cell type: primary human keratinocytes
tissue: neonatal foreskin
|
---
|
| Sample_geo_accession | GSM960297
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | patient sample
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in Keratinocyte Serum Free medium
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960297/suppl/GSM960297_hyb12865.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
GSM960298 | GPL570 |
|
24-PHK HPMPC c
|
PHK cells, 72h growth + 50µg/ml cidofovir
|
cell type: primary human keratinocytes
tissue: neonatal foreskin
|
---
|
| Sample_geo_accession | GSM960298
| | Sample_status | Public on Jul 03 2013
| | Sample_submission_date | Jul 12 2012
| | Sample_last_update_date | Jul 03 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | patient sample
| | Sample_treatment_protocol_ch1 | attached cells (24 h after passaging), grown for 72 h in renewed medium + 50 µg/ml cidofovir
| | Sample_growth_protocol_ch1 | cultured at 37°C, 5% CO2 in Keratinocyte Serum Free medium
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
| | Sample_hyb_protocol | A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
| | Sample_scan_protocol | To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
| | Sample_data_processing | Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM960nnn/GSM960298/suppl/GSM960298_hyb12866.CEL.gz
| | Sample_series_id | GSE39293
| | Sample_data_row_count | 54675
| | |
|
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