Search results for the GEO ID: GSE13763  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM346594 | GPL570 |
|
shCXCR4 (I) -1
|
human ovarian cancer cell line IGROV-1
|
IGROV transfected with shCXCR4 I
|
IGROV transfected with shCXCR4 I
|
| Sample_geo_accession | GSM346594
| | Sample_status | Public on Nov 29 2008
| | Sample_submission_date | Nov 28 2008
| | Sample_last_update_date | Nov 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IGROV-1 cells were transfected with SUPER RNAi™ plasmids containing two different shRNA sequences targeting CXCR4, or a control plasmid containg scrambled RNA (IGROV-Mock). Cells were transfected using Lipofectamin 2000 (Invitrogen, UK) following the manufauctures's instruction. Antibiotic selection for stable cell lines started 48 hours in 4 µg/ml puromycin (Sigma, UK) for 30 days. IGROV-Mock were a pool of clones whereas individual clones of shCXCR4 cells were selected.
| | Sample_growth_protocol_ch1 | The human ovarian cancer cell line IGROV-1 (from ATCC, Rockville, MD, USA) were cultured in endotoxin-free RPMI 1640 medium supplemented with 3.7 g/l NaHCO3 and 10 % FCS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed and purified further with the RNeasy kit (Qiagen) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 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 GeneChip human U133plus2.0 expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000G.
| | Sample_data_processing | Three Affymetrix data sets were obtained from triplicate samples of IGROV-1, IGROV-Mock and shCXCR4 I and II cells. Data were analysed using Bioconductor 1.9 (http://bioconductor.org) running on R 2.6.0. Probeset expression measures were calculated using the Affymetrix package's Robust Multichip Average (RMA) default method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hagen,,Kulbe
| | Sample_contact_email | h.kulbe@qmul.ac.uk
| | Sample_contact_department | Centre for Cancer and Inflammation
| | Sample_contact_institute | Institute of Cancer and the CR-UK Clinical Centre, Barts and The London School of Medicine and Dentistry
| | Sample_contact_address | Charterhouse Square
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | EC1M 6BQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346594/suppl/GSM346594.CEL.gz
| | Sample_series_id | GSE13763
| | Sample_data_row_count | 54675
| | |
|
GSM346595 | GPL570 |
|
shCXCR4 (I) -2
|
human ovarian cancer cell line IGROV-1
|
IGROV transfected with shCXCR4 I
|
IGROV transfected with shCXCR4 I
|
| Sample_geo_accession | GSM346595
| | Sample_status | Public on Nov 29 2008
| | Sample_submission_date | Nov 28 2008
| | Sample_last_update_date | Nov 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IGROV-1 cells were transfected with SUPER RNAi™ plasmids containing two different shRNA sequences targeting CXCR4, or a control plasmid containg scrambled RNA (IGROV-Mock). Cells were transfected using Lipofectamin 2000 (Invitrogen, UK) following the manufauctures's instruction. Antibiotic selection for stable cell lines started 48 hours in 4 µg/ml puromycin (Sigma, UK) for 30 days. IGROV-Mock were a pool of clones whereas individual clones of shCXCR4 cells were selected.
| | Sample_growth_protocol_ch1 | The human ovarian cancer cell line IGROV-1 (from ATCC, Rockville, MD, USA) were cultured in endotoxin-free RPMI 1640 medium supplemented with 3.7 g/l NaHCO3 and 10 % FCS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed and purified further with the RNeasy kit (Qiagen) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 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 GeneChip human U133plus2.0 expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000G.
| | Sample_data_processing | Three Affymetrix data sets were obtained from triplicate samples of IGROV-1, IGROV-Mock and shCXCR4 I and II cells. Data were analysed using Bioconductor 1.9 (http://bioconductor.org) running on R 2.6.0. Probeset expression measures were calculated using the Affymetrix package's Robust Multichip Average (RMA) default method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hagen,,Kulbe
| | Sample_contact_email | h.kulbe@qmul.ac.uk
| | Sample_contact_department | Centre for Cancer and Inflammation
| | Sample_contact_institute | Institute of Cancer and the CR-UK Clinical Centre, Barts and The London School of Medicine and Dentistry
| | Sample_contact_address | Charterhouse Square
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | EC1M 6BQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346595/suppl/GSM346595.CEL.gz
| | Sample_series_id | GSE13763
| | Sample_data_row_count | 54675
| | |
|
GSM346596 | GPL570 |
|
shCXCR4 (I) -3
|
human ovarian cancer cell line IGROV-1
|
IGROV transfected with shCXCR4 I
|
IGROV transfected with shCXCR4 I
|
| Sample_geo_accession | GSM346596
| | Sample_status | Public on Nov 29 2008
| | Sample_submission_date | Nov 28 2008
| | Sample_last_update_date | Nov 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IGROV-1 cells were transfected with SUPER RNAi™ plasmids containing two different shRNA sequences targeting CXCR4, or a control plasmid containg scrambled RNA (IGROV-Mock). Cells were transfected using Lipofectamin 2000 (Invitrogen, UK) following the manufauctures's instruction. Antibiotic selection for stable cell lines started 48 hours in 4 µg/ml puromycin (Sigma, UK) for 30 days. IGROV-Mock were a pool of clones whereas individual clones of shCXCR4 cells were selected.
| | Sample_growth_protocol_ch1 | The human ovarian cancer cell line IGROV-1 (from ATCC, Rockville, MD, USA) were cultured in endotoxin-free RPMI 1640 medium supplemented with 3.7 g/l NaHCO3 and 10 % FCS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed and purified further with the RNeasy kit (Qiagen) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 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 GeneChip human U133plus2.0 expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000G.
| | Sample_data_processing | Three Affymetrix data sets were obtained from triplicate samples of IGROV-1, IGROV-Mock and shCXCR4 I and II cells. Data were analysed using Bioconductor 1.9 (http://bioconductor.org) running on R 2.6.0. Probeset expression measures were calculated using the Affymetrix package's Robust Multichip Average (RMA) default method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hagen,,Kulbe
| | Sample_contact_email | h.kulbe@qmul.ac.uk
| | Sample_contact_department | Centre for Cancer and Inflammation
| | Sample_contact_institute | Institute of Cancer and the CR-UK Clinical Centre, Barts and The London School of Medicine and Dentistry
| | Sample_contact_address | Charterhouse Square
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | EC1M 6BQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346596/suppl/GSM346596.CEL.gz
| | Sample_series_id | GSE13763
| | Sample_data_row_count | 54675
| | |
|
GSM346597 | GPL570 |
|
shCXCR4 (II) -1
|
human ovarian cancer cell line IGROV-1
|
IGROV transfected with shCXCR4 II
|
IGROV transfected with shCXCR4 II
|
| Sample_geo_accession | GSM346597
| | Sample_status | Public on Nov 29 2008
| | Sample_submission_date | Nov 28 2008
| | Sample_last_update_date | Nov 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IGROV-1 cells were transfected with SUPER RNAi™ plasmids containing two different shRNA sequences targeting CXCR4, or a control plasmid containg scrambled RNA (IGROV-Mock). Cells were transfected using Lipofectamin 2000 (Invitrogen, UK) following the manufauctures's instruction. Antibiotic selection for stable cell lines started 48 hours in 4 µg/ml puromycin (Sigma, UK) for 30 days. IGROV-Mock were a pool of clones whereas individual clones of shCXCR4 cells were selected.
| | Sample_growth_protocol_ch1 | The human ovarian cancer cell line IGROV-1 (from ATCC, Rockville, MD, USA) were cultured in endotoxin-free RPMI 1640 medium supplemented with 3.7 g/l NaHCO3 and 10 % FCS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed and purified further with the RNeasy kit (Qiagen) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 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 GeneChip human U133plus2.0 expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000G.
| | Sample_data_processing | Three Affymetrix data sets were obtained from triplicate samples of IGROV-1, IGROV-Mock and shCXCR4 I and II cells. Data were analysed using Bioconductor 1.9 (http://bioconductor.org) running on R 2.6.0. Probeset expression measures were calculated using the Affymetrix package's Robust Multichip Average (RMA) default method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hagen,,Kulbe
| | Sample_contact_email | h.kulbe@qmul.ac.uk
| | Sample_contact_department | Centre for Cancer and Inflammation
| | Sample_contact_institute | Institute of Cancer and the CR-UK Clinical Centre, Barts and The London School of Medicine and Dentistry
| | Sample_contact_address | Charterhouse Square
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | EC1M 6BQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346597/suppl/GSM346597.CEL.gz
| | Sample_series_id | GSE13763
| | Sample_data_row_count | 54675
| | |
|
GSM346598 | GPL570 |
|
shCXCR4 (II) -2
|
human ovarian cancer cell line IGROV-1
|
IGROV transfected with shCXCR4 II
|
IGROV transfected with shCXCR4 II
|
| Sample_geo_accession | GSM346598
| | Sample_status | Public on Nov 29 2008
| | Sample_submission_date | Nov 28 2008
| | Sample_last_update_date | Nov 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IGROV-1 cells were transfected with SUPER RNAi™ plasmids containing two different shRNA sequences targeting CXCR4, or a control plasmid containg scrambled RNA (IGROV-Mock). Cells were transfected using Lipofectamin 2000 (Invitrogen, UK) following the manufauctures's instruction. Antibiotic selection for stable cell lines started 48 hours in 4 µg/ml puromycin (Sigma, UK) for 30 days. IGROV-Mock were a pool of clones whereas individual clones of shCXCR4 cells were selected.
| | Sample_growth_protocol_ch1 | The human ovarian cancer cell line IGROV-1 (from ATCC, Rockville, MD, USA) were cultured in endotoxin-free RPMI 1640 medium supplemented with 3.7 g/l NaHCO3 and 10 % FCS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed and purified further with the RNeasy kit (Qiagen) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 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 GeneChip human U133plus2.0 expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000G.
| | Sample_data_processing | Three Affymetrix data sets were obtained from triplicate samples of IGROV-1, IGROV-Mock and shCXCR4 I and II cells. Data were analysed using Bioconductor 1.9 (http://bioconductor.org) running on R 2.6.0. Probeset expression measures were calculated using the Affymetrix package's Robust Multichip Average (RMA) default method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hagen,,Kulbe
| | Sample_contact_email | h.kulbe@qmul.ac.uk
| | Sample_contact_department | Centre for Cancer and Inflammation
| | Sample_contact_institute | Institute of Cancer and the CR-UK Clinical Centre, Barts and The London School of Medicine and Dentistry
| | Sample_contact_address | Charterhouse Square
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | EC1M 6BQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346598/suppl/GSM346598.CEL.gz
| | Sample_series_id | GSE13763
| | Sample_data_row_count | 54675
| | |
|
GSM346599 | GPL570 |
|
shCXCR4 (II) -3
|
human ovarian cancer cell line IGROV-1
|
IGROV transfected with shCXCR4 II
|
IGROV transfected with shCXCR4 II
|
| Sample_geo_accession | GSM346599
| | Sample_status | Public on Nov 29 2008
| | Sample_submission_date | Nov 28 2008
| | Sample_last_update_date | Nov 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IGROV-1 cells were transfected with SUPER RNAi™ plasmids containing two different shRNA sequences targeting CXCR4, or a control plasmid containg scrambled RNA (IGROV-Mock). Cells were transfected using Lipofectamin 2000 (Invitrogen, UK) following the manufauctures's instruction. Antibiotic selection for stable cell lines started 48 hours in 4 µg/ml puromycin (Sigma, UK) for 30 days. IGROV-Mock were a pool of clones whereas individual clones of shCXCR4 cells were selected.
| | Sample_growth_protocol_ch1 | The human ovarian cancer cell line IGROV-1 (from ATCC, Rockville, MD, USA) were cultured in endotoxin-free RPMI 1640 medium supplemented with 3.7 g/l NaHCO3 and 10 % FCS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed and purified further with the RNeasy kit (Qiagen) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 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 GeneChip human U133plus2.0 expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000G.
| | Sample_data_processing | Three Affymetrix data sets were obtained from triplicate samples of IGROV-1, IGROV-Mock and shCXCR4 I and II cells. Data were analysed using Bioconductor 1.9 (http://bioconductor.org) running on R 2.6.0. Probeset expression measures were calculated using the Affymetrix package's Robust Multichip Average (RMA) default method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hagen,,Kulbe
| | Sample_contact_email | h.kulbe@qmul.ac.uk
| | Sample_contact_department | Centre for Cancer and Inflammation
| | Sample_contact_institute | Institute of Cancer and the CR-UK Clinical Centre, Barts and The London School of Medicine and Dentistry
| | Sample_contact_address | Charterhouse Square
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | EC1M 6BQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346599/suppl/GSM346599.CEL.gz
| | Sample_series_id | GSE13763
| | Sample_data_row_count | 54675
| | |
|
GSM346600 | GPL570 |
|
IGROV- 1
|
human ovarian cancer cell line IGROV-1
|
Parental IGROV
|
Parental IGROV
|
| Sample_geo_accession | GSM346600
| | Sample_status | Public on Nov 29 2008
| | Sample_submission_date | Nov 28 2008
| | Sample_last_update_date | Nov 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IGROV-1 cells were transfected with SUPER RNAi™ plasmids containing two different shRNA sequences targeting CXCR4, or a control plasmid containg scrambled RNA (IGROV-Mock). Cells were transfected using Lipofectamin 2000 (Invitrogen, UK) following the manufauctures's instruction. Antibiotic selection for stable cell lines started 48 hours in 4 µg/ml puromycin (Sigma, UK) for 30 days. IGROV-Mock were a pool of clones whereas individual clones of shCXCR4 cells were selected.
| | Sample_growth_protocol_ch1 | The human ovarian cancer cell line IGROV-1 (from ATCC, Rockville, MD, USA) were cultured in endotoxin-free RPMI 1640 medium supplemented with 3.7 g/l NaHCO3 and 10 % FCS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed and purified further with the RNeasy kit (Qiagen) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 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 GeneChip human U133plus2.0 expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000G.
| | Sample_data_processing | Three Affymetrix data sets were obtained from triplicate samples of IGROV-1, IGROV-Mock and shCXCR4 I and II cells. Data were analysed using Bioconductor 1.9 (http://bioconductor.org) running on R 2.6.0. Probeset expression measures were calculated using the Affymetrix package's Robust Multichip Average (RMA) default method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hagen,,Kulbe
| | Sample_contact_email | h.kulbe@qmul.ac.uk
| | Sample_contact_department | Centre for Cancer and Inflammation
| | Sample_contact_institute | Institute of Cancer and the CR-UK Clinical Centre, Barts and The London School of Medicine and Dentistry
| | Sample_contact_address | Charterhouse Square
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | EC1M 6BQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346600/suppl/GSM346600.CEL.gz
| | Sample_series_id | GSE13763
| | Sample_data_row_count | 54675
| | |
|
GSM346601 | GPL570 |
|
IGROV- 2
|
human ovarian cancer cell line IGROV-1
|
Parental IGROV
|
Parental IGROV
|
| Sample_geo_accession | GSM346601
| | Sample_status | Public on Nov 29 2008
| | Sample_submission_date | Nov 28 2008
| | Sample_last_update_date | Nov 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IGROV-1 cells were transfected with SUPER RNAi™ plasmids containing two different shRNA sequences targeting CXCR4, or a control plasmid containg scrambled RNA (IGROV-Mock). Cells were transfected using Lipofectamin 2000 (Invitrogen, UK) following the manufauctures's instruction. Antibiotic selection for stable cell lines started 48 hours in 4 µg/ml puromycin (Sigma, UK) for 30 days. IGROV-Mock were a pool of clones whereas individual clones of shCXCR4 cells were selected.
| | Sample_growth_protocol_ch1 | The human ovarian cancer cell line IGROV-1 (from ATCC, Rockville, MD, USA) were cultured in endotoxin-free RPMI 1640 medium supplemented with 3.7 g/l NaHCO3 and 10 % FCS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed and purified further with the RNeasy kit (Qiagen) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 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 GeneChip human U133plus2.0 expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000G.
| | Sample_data_processing | Three Affymetrix data sets were obtained from triplicate samples of IGROV-1, IGROV-Mock and shCXCR4 I and II cells. Data were analysed using Bioconductor 1.9 (http://bioconductor.org) running on R 2.6.0. Probeset expression measures were calculated using the Affymetrix package's Robust Multichip Average (RMA) default method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hagen,,Kulbe
| | Sample_contact_email | h.kulbe@qmul.ac.uk
| | Sample_contact_department | Centre for Cancer and Inflammation
| | Sample_contact_institute | Institute of Cancer and the CR-UK Clinical Centre, Barts and The London School of Medicine and Dentistry
| | Sample_contact_address | Charterhouse Square
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | EC1M 6BQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346601/suppl/GSM346601.CEL.gz
| | Sample_series_id | GSE13763
| | Sample_data_row_count | 54675
| | |
|
GSM346602 | GPL570 |
|
IGROV- 3
|
human ovarian cancer cell line IGROV-1
|
Parental IGROV
|
Parental IGROV
|
| Sample_geo_accession | GSM346602
| | Sample_status | Public on Nov 29 2008
| | Sample_submission_date | Nov 28 2008
| | Sample_last_update_date | Nov 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IGROV-1 cells were transfected with SUPER RNAi™ plasmids containing two different shRNA sequences targeting CXCR4, or a control plasmid containg scrambled RNA (IGROV-Mock). Cells were transfected using Lipofectamin 2000 (Invitrogen, UK) following the manufauctures's instruction. Antibiotic selection for stable cell lines started 48 hours in 4 µg/ml puromycin (Sigma, UK) for 30 days. IGROV-Mock were a pool of clones whereas individual clones of shCXCR4 cells were selected.
| | Sample_growth_protocol_ch1 | The human ovarian cancer cell line IGROV-1 (from ATCC, Rockville, MD, USA) were cultured in endotoxin-free RPMI 1640 medium supplemented with 3.7 g/l NaHCO3 and 10 % FCS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed and purified further with the RNeasy kit (Qiagen) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 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 GeneChip human U133plus2.0 expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000G.
| | Sample_data_processing | Three Affymetrix data sets were obtained from triplicate samples of IGROV-1, IGROV-Mock and shCXCR4 I and II cells. Data were analysed using Bioconductor 1.9 (http://bioconductor.org) running on R 2.6.0. Probeset expression measures were calculated using the Affymetrix package's Robust Multichip Average (RMA) default method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hagen,,Kulbe
| | Sample_contact_email | h.kulbe@qmul.ac.uk
| | Sample_contact_department | Centre for Cancer and Inflammation
| | Sample_contact_institute | Institute of Cancer and the CR-UK Clinical Centre, Barts and The London School of Medicine and Dentistry
| | Sample_contact_address | Charterhouse Square
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | EC1M 6BQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346602/suppl/GSM346602.CEL.gz
| | Sample_series_id | GSE13763
| | Sample_data_row_count | 54675
| | |
|
GSM346603 | GPL570 |
|
IGROV - Mock -1
|
human ovarian cancer cell line IGROV-1
|
IGROV transfected with scrambled RNA
|
IGROV transfected with scrambled RNA
|
| Sample_geo_accession | GSM346603
| | Sample_status | Public on Nov 29 2008
| | Sample_submission_date | Nov 28 2008
| | Sample_last_update_date | Nov 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IGROV-1 cells were transfected with SUPER RNAi™ plasmids containing two different shRNA sequences targeting CXCR4, or a control plasmid containg scrambled RNA (IGROV-Mock). Cells were transfected using Lipofectamin 2000 (Invitrogen, UK) following the manufauctures's instruction. Antibiotic selection for stable cell lines started 48 hours in 4 µg/ml puromycin (Sigma, UK) for 30 days. IGROV-Mock were a pool of clones whereas individual clones of shCXCR4 cells were selected.
| | Sample_growth_protocol_ch1 | The human ovarian cancer cell line IGROV-1 (from ATCC, Rockville, MD, USA) were cultured in endotoxin-free RPMI 1640 medium supplemented with 3.7 g/l NaHCO3 and 10 % FCS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed and purified further with the RNeasy kit (Qiagen) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 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 GeneChip human U133plus2.0 expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000G.
| | Sample_data_processing | Three Affymetrix data sets were obtained from triplicate samples of IGROV-1, IGROV-Mock and shCXCR4 I and II cells. Data were analysed using Bioconductor 1.9 (http://bioconductor.org) running on R 2.6.0. Probeset expression measures were calculated using the Affymetrix package's Robust Multichip Average (RMA) default method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hagen,,Kulbe
| | Sample_contact_email | h.kulbe@qmul.ac.uk
| | Sample_contact_department | Centre for Cancer and Inflammation
| | Sample_contact_institute | Institute of Cancer and the CR-UK Clinical Centre, Barts and The London School of Medicine and Dentistry
| | Sample_contact_address | Charterhouse Square
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | EC1M 6BQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346603/suppl/GSM346603.CEL.gz
| | Sample_series_id | GSE13763
| | Sample_data_row_count | 54675
| | |
|
GSM346604 | GPL570 |
|
IGROV - Mock -2
|
human ovarian cancer cell line IGROV-1
|
IGROV transfected with scrambled RNA
|
IGROV transfected with scrambled RNA
|
| Sample_geo_accession | GSM346604
| | Sample_status | Public on Nov 29 2008
| | Sample_submission_date | Nov 28 2008
| | Sample_last_update_date | Nov 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IGROV-1 cells were transfected with SUPER RNAi™ plasmids containing two different shRNA sequences targeting CXCR4, or a control plasmid containg scrambled RNA (IGROV-Mock). Cells were transfected using Lipofectamin 2000 (Invitrogen, UK) following the manufauctures's instruction. Antibiotic selection for stable cell lines started 48 hours in 4 µg/ml puromycin (Sigma, UK) for 30 days. IGROV-Mock were a pool of clones whereas individual clones of shCXCR4 cells were selected.
| | Sample_growth_protocol_ch1 | The human ovarian cancer cell line IGROV-1 (from ATCC, Rockville, MD, USA) were cultured in endotoxin-free RPMI 1640 medium supplemented with 3.7 g/l NaHCO3 and 10 % FCS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed and purified further with the RNeasy kit (Qiagen) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 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 GeneChip human U133plus2.0 expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000G.
| | Sample_data_processing | Three Affymetrix data sets were obtained from triplicate samples of IGROV-1, IGROV-Mock and shCXCR4 I and II cells. Data were analysed using Bioconductor 1.9 (http://bioconductor.org) running on R 2.6.0. Probeset expression measures were calculated using the Affymetrix package's Robust Multichip Average (RMA) default method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hagen,,Kulbe
| | Sample_contact_email | h.kulbe@qmul.ac.uk
| | Sample_contact_department | Centre for Cancer and Inflammation
| | Sample_contact_institute | Institute of Cancer and the CR-UK Clinical Centre, Barts and The London School of Medicine and Dentistry
| | Sample_contact_address | Charterhouse Square
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | EC1M 6BQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346604/suppl/GSM346604.CEL.gz
| | Sample_series_id | GSE13763
| | Sample_data_row_count | 54675
| | |
|
GSM346605 | GPL570 |
|
IGROV - Mock -3
|
human ovarian cancer cell line IGROV-1
|
IGROV transfected with scrambled RNA
|
IGROV transfected with scrambled RNA
|
| Sample_geo_accession | GSM346605
| | Sample_status | Public on Nov 29 2008
| | Sample_submission_date | Nov 28 2008
| | Sample_last_update_date | Nov 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | IGROV-1 cells were transfected with SUPER RNAi™ plasmids containing two different shRNA sequences targeting CXCR4, or a control plasmid containg scrambled RNA (IGROV-Mock). Cells were transfected using Lipofectamin 2000 (Invitrogen, UK) following the manufauctures's instruction. Antibiotic selection for stable cell lines started 48 hours in 4 µg/ml puromycin (Sigma, UK) for 30 days. IGROV-Mock were a pool of clones whereas individual clones of shCXCR4 cells were selected.
| | Sample_growth_protocol_ch1 | The human ovarian cancer cell line IGROV-1 (from ATCC, Rockville, MD, USA) were cultured in endotoxin-free RPMI 1640 medium supplemented with 3.7 g/l NaHCO3 and 10 % FCS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed and purified further with the RNeasy kit (Qiagen) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 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 GeneChip human U133plus2.0 expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000G.
| | Sample_data_processing | Three Affymetrix data sets were obtained from triplicate samples of IGROV-1, IGROV-Mock and shCXCR4 I and II cells. Data were analysed using Bioconductor 1.9 (http://bioconductor.org) running on R 2.6.0. Probeset expression measures were calculated using the Affymetrix package's Robust Multichip Average (RMA) default method.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hagen,,Kulbe
| | Sample_contact_email | h.kulbe@qmul.ac.uk
| | Sample_contact_department | Centre for Cancer and Inflammation
| | Sample_contact_institute | Institute of Cancer and the CR-UK Clinical Centre, Barts and The London School of Medicine and Dentistry
| | Sample_contact_address | Charterhouse Square
| | Sample_contact_city | London
| | Sample_contact_zip/postal_code | EC1M 6BQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM346nnn/GSM346605/suppl/GSM346605.CEL.gz
| | Sample_series_id | GSE13763
| | Sample_data_row_count | 54675
| | |
|
| |
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