Search results for the GEO ID: GSE17480  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM435978 | GPL570 |
|
CD34+ cells without fenretinide treatment from CML32
|
CD34+ cells from the patient (CML32)
|
disease status: CML chronic phase (CP)
cell source: leukapheresis products (LP)
cell type: CD34+ mononuclear cells
|
Untreated CD34+ cells isolated from the patient CML32, harvested after 48h in culture
|
| Sample_geo_accession | GSM435978
| | Sample_status | Public on Dec 01 2009
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CML CD34+ cells treated with or without 4 µM fenretinide were maintained in culture for 48 hours prior to hybridization.
| | Sample_growth_protocol_ch1 | Fresh bone marrow (BM) cells or leukapheresis products (LP) were obtained from four CML patients with informed consent and approval of Institutional Review Board at the School of Medicine in Shanghai Jiao Tong University. Mononuclear cells were isolated by Ficoll density gradient centrifugation. CD34+ cells were enriched using EasySep® Human CD34 Positive Selection kit (Stem Cell Technologies, Vancouver, BC) according to the manufacturer's instructions. The purity of CD34+ cells ranged between 92 and 98% in all samples determined by flow cytometry. The CD34+ cells were cultured in a STEMPRO-34® SFM Complete Medium (Invitrogen, Carlsbad, CA) supplemented with growth factors (PeproTech, London, UK). The growth factors consisted of GM-CSF (200 pg/mL), G-CSF (1 ng/mL); SCF (200 pg/mL); LIF (50 pg/mL), MIP-1α (200 pg/mL) and IL-6 (1 ng/mL).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed 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 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The fragmented, biotinylated cRNA were used for hybridization at 45C for 17 hours with Affymetrix HG-U133 Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the arrays.
| | Sample_data_processing | Raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization. The normalized expression data was subsequently imported into Linear Models for Microarray Data (LIMMA) bioconductor library for the detection of differentially expressed probesets using paired t-tests for the fenretinide versus control comparison across 4 CML patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435978/suppl/GSM435978.CEL.gz
| | Sample_series_id | GSE17480
| | Sample_data_row_count | 54675
| | |
|
GSM435979 | GPL570 |
|
CD34+ cells with fenretinide treatment from CML32
|
CD34+ cells from the patient (CML32)
|
disease status: CML chronic phase (CP)
cell source: leukapheresis products (LP)
cell type: CD34+ mononuclear cells
|
Fenretinide-treated CD34+ cells isolated from the patient CML32, harvested after 48h in culture
|
| Sample_geo_accession | GSM435979
| | Sample_status | Public on Dec 01 2009
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CML CD34+ cells treated with or without 4 µM fenretinide were maintained in culture for 48 hours prior to hybridization.
| | Sample_growth_protocol_ch1 | Fresh bone marrow (BM) cells or leukapheresis products (LP) were obtained from four CML patients with informed consent and approval of Institutional Review Board at the School of Medicine in Shanghai Jiao Tong University. Mononuclear cells were isolated by Ficoll density gradient centrifugation. CD34+ cells were enriched using EasySep® Human CD34 Positive Selection kit (Stem Cell Technologies, Vancouver, BC) according to the manufacturer's instructions. The purity of CD34+ cells ranged between 92 and 98% in all samples determined by flow cytometry. The CD34+ cells were cultured in a STEMPRO-34® SFM Complete Medium (Invitrogen, Carlsbad, CA) supplemented with growth factors (PeproTech, London, UK). The growth factors consisted of GM-CSF (200 pg/mL), G-CSF (1 ng/mL); SCF (200 pg/mL); LIF (50 pg/mL), MIP-1α (200 pg/mL) and IL-6 (1 ng/mL).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed 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 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The fragmented, biotinylated cRNA were used for hybridization at 45C for 17 hours with Affymetrix HG-U133 Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the arrays.
| | Sample_data_processing | Raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization. The normalized expression data was subsequently imported into Linear Models for Microarray Data (LIMMA) bioconductor library for the detection of differentially expressed probesets using paired t-tests for the fenretinide versus control comparison across 4 CML patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435979/suppl/GSM435979.CEL.gz
| | Sample_series_id | GSE17480
| | Sample_data_row_count | 54675
| | |
|
GSM435980 | GPL570 |
|
CD34+ cells without fenretinide treatment from CML33
|
CD34+ cells from the patient (CML33)
|
disease status: CML chronic phase (CP)
cell source: leukapheresis products (LP)
cell type: CD34+ mononuclear cells
|
Untreated CD34+ cells isolated from the patient CML33, harvested after 48h in culture
|
| Sample_geo_accession | GSM435980
| | Sample_status | Public on Dec 01 2009
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CML CD34+ cells treated with or without 4 µM fenretinide were maintained in culture for 48 hours prior to hybridization.
| | Sample_growth_protocol_ch1 | Fresh bone marrow (BM) cells or leukapheresis products (LP) were obtained from four CML patients with informed consent and approval of Institutional Review Board at the School of Medicine in Shanghai Jiao Tong University. Mononuclear cells were isolated by Ficoll density gradient centrifugation. CD34+ cells were enriched using EasySep® Human CD34 Positive Selection kit (Stem Cell Technologies, Vancouver, BC) according to the manufacturer's instructions. The purity of CD34+ cells ranged between 92 and 98% in all samples determined by flow cytometry. The CD34+ cells were cultured in a STEMPRO-34® SFM Complete Medium (Invitrogen, Carlsbad, CA) supplemented with growth factors (PeproTech, London, UK). The growth factors consisted of GM-CSF (200 pg/mL), G-CSF (1 ng/mL); SCF (200 pg/mL); LIF (50 pg/mL), MIP-1α (200 pg/mL) and IL-6 (1 ng/mL).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed 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 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The fragmented, biotinylated cRNA were used for hybridization at 45C for 17 hours with Affymetrix HG-U133 Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the arrays.
| | Sample_data_processing | Raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization. The normalized expression data was subsequently imported into Linear Models for Microarray Data (LIMMA) bioconductor library for the detection of differentially expressed probesets using paired t-tests for the fenretinide versus control comparison across 4 CML patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435980/suppl/GSM435980.CEL.gz
| | Sample_series_id | GSE17480
| | Sample_data_row_count | 54675
| | |
|
GSM435981 | GPL570 |
|
CD34+ cells with fenretinide treatment from CML33
|
CD34+ cells from the patient (CML33)
|
disease status: CML chronic phase (CP)
cell source: leukapheresis products (LP)
cell type: CD34+ mononuclear cells
|
Fenretinide-treated CD34+ cells isolated from the patient CML33, harvested after 48h in culture
|
| Sample_geo_accession | GSM435981
| | Sample_status | Public on Dec 01 2009
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CML CD34+ cells treated with or without 4 µM fenretinide were maintained in culture for 48 hours prior to hybridization.
| | Sample_growth_protocol_ch1 | Fresh bone marrow (BM) cells or leukapheresis products (LP) were obtained from four CML patients with informed consent and approval of Institutional Review Board at the School of Medicine in Shanghai Jiao Tong University. Mononuclear cells were isolated by Ficoll density gradient centrifugation. CD34+ cells were enriched using EasySep® Human CD34 Positive Selection kit (Stem Cell Technologies, Vancouver, BC) according to the manufacturer's instructions. The purity of CD34+ cells ranged between 92 and 98% in all samples determined by flow cytometry. The CD34+ cells were cultured in a STEMPRO-34® SFM Complete Medium (Invitrogen, Carlsbad, CA) supplemented with growth factors (PeproTech, London, UK). The growth factors consisted of GM-CSF (200 pg/mL), G-CSF (1 ng/mL); SCF (200 pg/mL); LIF (50 pg/mL), MIP-1α (200 pg/mL) and IL-6 (1 ng/mL).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed 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 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The fragmented, biotinylated cRNA were used for hybridization at 45C for 17 hours with Affymetrix HG-U133 Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the arrays.
| | Sample_data_processing | Raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization. The normalized expression data was subsequently imported into Linear Models for Microarray Data (LIMMA) bioconductor library for the detection of differentially expressed probesets using paired t-tests for the fenretinide versus control comparison across 4 CML patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435981/suppl/GSM435981.CEL.gz
| | Sample_series_id | GSE17480
| | Sample_data_row_count | 54675
| | |
|
GSM435982 | GPL570 |
|
CD34+ cells without fenretinide treatment from CML34
|
CD34+ cells from the patient (CML34)
|
disease status: CML chronic phase (CP)
cell source: bone marrow (BM)
cell type: CD34+ mononuclear cells
|
Untreated CD34+ cells isolated from the patient CML34, harvested after 48h in culture
|
| Sample_geo_accession | GSM435982
| | Sample_status | Public on Dec 01 2009
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CML CD34+ cells treated with or without 4 µM fenretinide were maintained in culture for 48 hours prior to hybridization.
| | Sample_growth_protocol_ch1 | Fresh bone marrow (BM) cells or leukapheresis products (LP) were obtained from four CML patients with informed consent and approval of Institutional Review Board at the School of Medicine in Shanghai Jiao Tong University. Mononuclear cells were isolated by Ficoll density gradient centrifugation. CD34+ cells were enriched using EasySep® Human CD34 Positive Selection kit (Stem Cell Technologies, Vancouver, BC) according to the manufacturer's instructions. The purity of CD34+ cells ranged between 92 and 98% in all samples determined by flow cytometry. The CD34+ cells were cultured in a STEMPRO-34® SFM Complete Medium (Invitrogen, Carlsbad, CA) supplemented with growth factors (PeproTech, London, UK). The growth factors consisted of GM-CSF (200 pg/mL), G-CSF (1 ng/mL); SCF (200 pg/mL); LIF (50 pg/mL), MIP-1α (200 pg/mL) and IL-6 (1 ng/mL).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed 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 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The fragmented, biotinylated cRNA were used for hybridization at 45C for 17 hours with Affymetrix HG-U133 Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the arrays.
| | Sample_data_processing | Raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization. The normalized expression data was subsequently imported into Linear Models for Microarray Data (LIMMA) bioconductor library for the detection of differentially expressed probesets using paired t-tests for the fenretinide versus control comparison across 4 CML patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435982/suppl/GSM435982.CEL.gz
| | Sample_series_id | GSE17480
| | Sample_data_row_count | 54675
| | |
|
GSM435983 | GPL570 |
|
CD34+ cells with fenretinide treatment from CML34
|
CD34+ cells from the patient (CML34)
|
disease status: CML chronic phase (CP)
cell source: bone marrow (BM)
cell type: CD34+ mononuclear cells
|
Fenretinide-treated CD34+ cells isolated from the patient CML34, harvested after 48h in culture
|
| Sample_geo_accession | GSM435983
| | Sample_status | Public on Dec 01 2009
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CML CD34+ cells treated with or without 4 µM fenretinide were maintained in culture for 48 hours prior to hybridization.
| | Sample_growth_protocol_ch1 | Fresh bone marrow (BM) cells or leukapheresis products (LP) were obtained from four CML patients with informed consent and approval of Institutional Review Board at the School of Medicine in Shanghai Jiao Tong University. Mononuclear cells were isolated by Ficoll density gradient centrifugation. CD34+ cells were enriched using EasySep® Human CD34 Positive Selection kit (Stem Cell Technologies, Vancouver, BC) according to the manufacturer's instructions. The purity of CD34+ cells ranged between 92 and 98% in all samples determined by flow cytometry. The CD34+ cells were cultured in a STEMPRO-34® SFM Complete Medium (Invitrogen, Carlsbad, CA) supplemented with growth factors (PeproTech, London, UK). The growth factors consisted of GM-CSF (200 pg/mL), G-CSF (1 ng/mL); SCF (200 pg/mL); LIF (50 pg/mL), MIP-1α (200 pg/mL) and IL-6 (1 ng/mL).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed 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 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The fragmented, biotinylated cRNA were used for hybridization at 45C for 17 hours with Affymetrix HG-U133 Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the arrays.
| | Sample_data_processing | Raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization. The normalized expression data was subsequently imported into Linear Models for Microarray Data (LIMMA) bioconductor library for the detection of differentially expressed probesets using paired t-tests for the fenretinide versus control comparison across 4 CML patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435983/suppl/GSM435983.CEL.gz
| | Sample_series_id | GSE17480
| | Sample_data_row_count | 54675
| | |
|
GSM435984 | GPL570 |
|
CD34+ cells without fenretinide treatment from CML35
|
CD34+ cells from the patient (CML35)
|
disease status: CML chronic phase (CP)
cell source: leukapheresis products (LP)
cell type: CD34+ mononuclear cells
|
Untreated CD34+ cells isolated from the patient CML35, harvested after 48h in culture
|
| Sample_geo_accession | GSM435984
| | Sample_status | Public on Dec 01 2009
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CML CD34+ cells treated with or without 4 µM fenretinide were maintained in culture for 48 hours prior to hybridization.
| | Sample_growth_protocol_ch1 | Fresh bone marrow (BM) cells or leukapheresis products (LP) were obtained from four CML patients with informed consent and approval of Institutional Review Board at the School of Medicine in Shanghai Jiao Tong University. Mononuclear cells were isolated by Ficoll density gradient centrifugation. CD34+ cells were enriched using EasySep® Human CD34 Positive Selection kit (Stem Cell Technologies, Vancouver, BC) according to the manufacturer's instructions. The purity of CD34+ cells ranged between 92 and 98% in all samples determined by flow cytometry. The CD34+ cells were cultured in a STEMPRO-34® SFM Complete Medium (Invitrogen, Carlsbad, CA) supplemented with growth factors (PeproTech, London, UK). The growth factors consisted of GM-CSF (200 pg/mL), G-CSF (1 ng/mL); SCF (200 pg/mL); LIF (50 pg/mL), MIP-1α (200 pg/mL) and IL-6 (1 ng/mL).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed 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 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The fragmented, biotinylated cRNA were used for hybridization at 45C for 17 hours with Affymetrix HG-U133 Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the arrays.
| | Sample_data_processing | Raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization. The normalized expression data was subsequently imported into Linear Models for Microarray Data (LIMMA) bioconductor library for the detection of differentially expressed probesets using paired t-tests for the fenretinide versus control comparison across 4 CML patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435984/suppl/GSM435984.CEL.gz
| | Sample_series_id | GSE17480
| | Sample_data_row_count | 54675
| | |
|
GSM435985 | GPL570 |
|
CD34+ cells with fenretinide treatment from CML35
|
CD34+ cells from the patient (CML35)
|
disease status: CML chronic phase (CP)
cell source: leukapheresis products (LP)
cell type: CD34+ mononuclear cells
|
Fenretinide-treated CD34+ cells isolated from the patient CML35, harvested after 48h in culture
|
| Sample_geo_accession | GSM435985
| | Sample_status | Public on Dec 01 2009
| | Sample_submission_date | Aug 03 2009
| | Sample_last_update_date | Aug 03 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CML CD34+ cells treated with or without 4 µM fenretinide were maintained in culture for 48 hours prior to hybridization.
| | Sample_growth_protocol_ch1 | Fresh bone marrow (BM) cells or leukapheresis products (LP) were obtained from four CML patients with informed consent and approval of Institutional Review Board at the School of Medicine in Shanghai Jiao Tong University. Mononuclear cells were isolated by Ficoll density gradient centrifugation. CD34+ cells were enriched using EasySep® Human CD34 Positive Selection kit (Stem Cell Technologies, Vancouver, BC) according to the manufacturer's instructions. The purity of CD34+ cells ranged between 92 and 98% in all samples determined by flow cytometry. The CD34+ cells were cultured in a STEMPRO-34® SFM Complete Medium (Invitrogen, Carlsbad, CA) supplemented with growth factors (PeproTech, London, UK). The growth factors consisted of GM-CSF (200 pg/mL), G-CSF (1 ng/mL); SCF (200 pg/mL); LIF (50 pg/mL), MIP-1α (200 pg/mL) and IL-6 (1 ng/mL).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed 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 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The fragmented, biotinylated cRNA were used for hybridization at 45C for 17 hours with Affymetrix HG-U133 Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | An affymetrix Gene Chip Scanner 3000 was used to scan the arrays.
| | Sample_data_processing | Raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization. The normalized expression data was subsequently imported into Linear Models for Microarray Data (LIMMA) bioconductor library for the detection of differentially expressed probesets using paired t-tests for the fenretinide versus control comparison across 4 CML patients.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Hai,,Fang
| | Sample_contact_email | hfang@cs.bris.ac.uk
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | University of Bristol
| | Sample_contact_address | Woodland Road
| | Sample_contact_city | Bristol
| | Sample_contact_zip/postal_code | BS8 1UB
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM435nnn/GSM435985/suppl/GSM435985.CEL.gz
| | Sample_series_id | GSE17480
| | Sample_data_row_count | 54675
| | |
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