Search results for the GEO ID: GSE19610  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM489097 | GPL96 |
|
Pt1_MDS_Decitabine_rep1
|
Pt1, MDS, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: male
age: 59
disease: MDS
karyotype: normal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489097
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489097/suppl/GSM489097.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489098 | GPL96 |
|
Pt1_MDS_Decitabine_rep2
|
Pt1, MDS, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: male
age: 59
disease: MDS
karyotype: normal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489098
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489098/suppl/GSM489098.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489099 | GPL96 |
|
Pt1_MDS_Decitabine_rep3
|
Pt1, MDS, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: male
age: 59
disease: MDS
karyotype: normal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489099
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489099/suppl/GSM489099.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489100 | GPL96 |
|
Pt1_MDS_mock_rep1
|
Pt1, MDS, mock treatment
|
cell type: bone marrow CD34+
gender: male
age: 59
disease: MDS
karyotype: normal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro mock treatment for 72 hours
|
| Sample_geo_accession | GSM489100
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489100/suppl/GSM489100.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489101 | GPL96 |
|
Pt1_MDS_mock_rep2
|
Pt1, MDS, mock treatment
|
cell type: bone marrow CD34+
gender: male
age: 59
disease: MDS
karyotype: normal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro mock treatment for 72 hours
|
| Sample_geo_accession | GSM489101
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489101/suppl/GSM489101.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489102 | GPL96 |
|
Pt2_MDS_Decitabine_rep1
|
Pt2, MDS, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: female
age: 71
disease: MDS
karyotype: abnormal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489102
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489102/suppl/GSM489102.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489103 | GPL96 |
|
Pt2_MDS_Decitabine_rep2
|
Pt2, MDS, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: female
age: 71
disease: MDS
karyotype: abnormal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489103
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489103/suppl/GSM489103.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489104 | GPL96 |
|
Pt2_MDS_Decitabine_rep3
|
Pt2, MDS, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: female
age: 71
disease: MDS
karyotype: abnormal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489104
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489104/suppl/GSM489104.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489105 | GPL96 |
|
Pt2_MDS_mock_rep1
|
Pt2, MDS, mock treatment
|
cell type: bone marrow CD34+
gender: female
age: 71
disease: MDS
karyotype: abnormal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro mock treatment for 72 hours
|
| Sample_geo_accession | GSM489105
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489105/suppl/GSM489105.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489106 | GPL96 |
|
Pt2_MDS_mock_rep2
|
Pt2, MDS, mock treatment
|
cell type: bone marrow CD34+
gender: female
age: 71
disease: MDS
karyotype: abnormal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro mock treatment for 72 hours
|
| Sample_geo_accession | GSM489106
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489106/suppl/GSM489106.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489107 | GPL96 |
|
Pt3_MDS_Decitabine_rep1
|
Pt3, MDS, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: female
age: 55
disease: MDS
karyotype: abnormal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489107
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489107/suppl/GSM489107.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489108 | GPL96 |
|
Pt3_MDS_Decitabine_rep2
|
Pt3, MDS, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: female
age: 55
disease: MDS
karyotype: abnormal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489108
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489108/suppl/GSM489108.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489109 | GPL96 |
|
Pt3_MDS_Decitabine_rep3
|
Pt3, MDS, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: female
age: 55
disease: MDS
karyotype: abnormal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489109
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489109/suppl/GSM489109.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489110 | GPL96 |
|
Pt3_MDS_mock_rep1
|
Pt3, MDS, mock treatment
|
cell type: bone marrow CD34+
gender: female
age: 55
disease: MDS
karyotype: abnormal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro mock treatment for 72 hours
|
| Sample_geo_accession | GSM489110
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489110/suppl/GSM489110.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489111 | GPL96 |
|
Pt3_MDS_mock_rep2
|
Pt3, MDS, mock treatment
|
cell type: bone marrow CD34+
gender: female
age: 55
disease: MDS
karyotype: abnormal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro mock treatment for 72 hours
|
| Sample_geo_accession | GSM489111
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489111/suppl/GSM489111.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489112 | GPL96 |
|
Pt4_MDS_Decitabine_rep1
|
Pt4, MDS, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: male
age: 76
disease: MDS
karyotype: normal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489112
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489112/suppl/GSM489112.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489113 | GPL96 |
|
Pt4_MDS_Decitabine_rep2
|
Pt4, MDS, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: male
age: 76
disease: MDS
karyotype: normal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489113
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489113/suppl/GSM489113.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489114 | GPL96 |
|
Pt4_MDS_Decitabine_rep3
|
Pt4, MDS, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: male
age: 76
disease: MDS
karyotype: normal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489114
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489114/suppl/GSM489114.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489115 | GPL96 |
|
Pt4_MDS_mock_rep1
|
Pt4, MDS, mock treatment
|
cell type: bone marrow CD34+
gender: male
age: 76
disease: MDS
karyotype: normal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro mock treatment for 72 hours
|
| Sample_geo_accession | GSM489115
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489115/suppl/GSM489115.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489116 | GPL96 |
|
Pt4_MDS_mock_rep2
|
Pt4, MDS, mock treatment
|
cell type: bone marrow CD34+
gender: male
age: 76
disease: MDS
karyotype: normal
|
Gene expression data from bone marrow myelodysplastic CD34+ cells after in vitro mock treatment for 72 hours
|
| Sample_geo_accession | GSM489116
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489116/suppl/GSM489116.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489117 | GPL96 |
|
Pt5_HL_Decitabine_rep1
|
Pt5, HL, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: male
age: 35
disease: HL
karyotype: normal
|
Gene expression data from bone marrow normal CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489117
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489117/suppl/GSM489117.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489118 | GPL96 |
|
Pt5_HL_Decitabine_rep2
|
Pt5, HL, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: male
age: 35
disease: HL
karyotype: normal
|
Gene expression data from bone marrow normal CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489118
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489118/suppl/GSM489118.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489119 | GPL96 |
|
Pt5_HL_Decitabine_rep3
|
Pt5, HL, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: male
age: 35
disease: HL
karyotype: normal
|
Gene expression data from bone marrow normal CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489119
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489119/suppl/GSM489119.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489120 | GPL96 |
|
Pt5_HL_mock_rep1
|
Pt5, HL, mock treatment
|
cell type: bone marrow CD34+
gender: male
age: 35
disease: HL
karyotype: normal
|
Gene expression data from bone marrow normal CD34+ cells after in vitro mock treatment for 72 hours
|
| Sample_geo_accession | GSM489120
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489120/suppl/GSM489120.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489121 | GPL96 |
|
Pt5_HL_mock_rep2
|
Pt5, HL, mock treatment
|
cell type: bone marrow CD34+
gender: male
age: 35
disease: HL
karyotype: normal
|
Gene expression data from bone marrow normal CD34+ cells after in vitro mock treatment for 72 hours
|
| Sample_geo_accession | GSM489121
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489121/suppl/GSM489121.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489122 | GPL96 |
|
Pt6_HL_Decitabine_rep1
|
Pt6, HL, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: female
age: 29
disease: HL
karyotype: normal
|
Gene expression data from bone marrow normal CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489122
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489122/suppl/GSM489122.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489123 | GPL96 |
|
Pt6_HL_Decitabine_rep2
|
Pt6, HL, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: female
age: 29
disease: HL
karyotype: normal
|
Gene expression data from bone marrow normal CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489123
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489123/suppl/GSM489123.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489124 | GPL96 |
|
Pt6_HL_Decitabine_rep3
|
Pt6, HL, 1 µM decitabine
|
cell type: bone marrow CD34+
gender: female
age: 29
disease: HL
karyotype: normal
|
Gene expression data from bone marrow normal CD34+ cells after in vitro treatment with 1μM decitabine for 72 hours
|
| Sample_geo_accession | GSM489124
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489124/suppl/GSM489124.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
| | |
|
GSM489125 | GPL96 |
|
Pt6_HL_mock_rep1
|
Pt6, HL, mock treatment
|
cell type: bone marrow CD34+
gender: female
age: 29
disease: HL
karyotype: normal
|
Gene expression data from bone marrow normal CD34+ cells after in vitro mock treatment for 72 hours
|
| Sample_geo_accession | GSM489125
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489125/suppl/GSM489125.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
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GSM489126 | GPL96 |
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Pt6_HL_mock_rep2
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Pt6, HL, mock treatment
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cell type: bone marrow CD34+
gender: female
age: 29
disease: HL
karyotype: normal
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Gene expression data from bone marrow normal CD34+ cells after in vitro mock treatment for 72 hours
|
| Sample_geo_accession | GSM489126
| | Sample_status | Public on Dec 23 2009
| | Sample_submission_date | Dec 22 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Decitabine (Sigma Aldrich) was dissolved in 10 mM stock solution in 50:50 Glacial Acetic Acid:1x Phosphate buffered saline (PBS) and stored at -20°C. A solution of 50:50 Glacial Acetic Acid: PBS without decitabine was used for the mock treatment. Decitabine was added to the culture medium to a final concentration of 1 µM for 72 hours, while the corresponding amount of solvent was added for the mock treated plates.
| | Sample_growth_protocol_ch1 | Freshly isolated bone marrow CD34+ cells were cultured at a concetration of 5-10x10E+04 cells per well in 24-well-plates for 24 hours before starting treatment. Culture conditions were: IMDM medium with 30% inactivated fetal bovine serum, 1X L-Glutamine, 1X Penicillin-Streptomycin, and a pool of growth factors including 10 ng/ml each of Stem Cell Factor, Flt3 ligand, IL3 and Thrombopoietin (Sigma Aldrich), at humidified atmosphere with 5% C02 at 37°C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | GeneChip® Two-Cycle Target Labeling and Control Reagents kit (Affymetrix) was used to amplify and label RNA, according to the manufacturer’s instructions.
| | Sample_hyb_protocol | Five μg of biotinilated cRNA were then hybridized on Affymetrix GeneChips HG-U133A. The hybridization, washing and staining were carried out as recommended by the manufacturer. We used 5 arrays for each patient: three replicates for decitabine treated CD34+ cells and two replicates for mock treated cells. Washes and staining were performed through the Fluidics Station 400.
| | Sample_scan_protocol | GeneChip® Scanner 3000 (Affymetrix) was used to measure the fluorescence intensity emitted by the labeled target. Raw data processing was performed by using the Affymetrix GeneChip® Operating Software (GCOS) 1.2 software
| | Sample_data_processing | Data were analyzed by the software Bioconductor (www.bioconductor.org and www.bioinformatica.unito.it) through the program RGui version 2.5.0, package oneChannelGUI. Intensity were represented by Raw Intensity Box Plot to visualize variation in cRNA loading. The Probe Level Model (PLM) was used for quality control and the function and graphs Relative Log Expression (RLE) and Normalized Unscaled Standard Errors (NUSE) were applied. Data were then normalized by GCRMA. The Principal Component Analysis (PCA) has been used to visualize data distribution and replicate quality. Data were then filtered for interquartile range IQR<0.25, and for intensity threshold of 100 in at least 50% arrays, resulting into 5714 filtered genes. The Bayesian method Linear Model Analysis of Microarray (Limma) was used to identify differentially expressed genes, by sorting data with p value <0.05 and log2 fold change >1. Contrasts were analyzed for diagnosis (MDS vs HL), karyotype (normal vs abnormal) and treatment (decitabine vs mock). Contrasts were visualized by Volcano Plots and lists of differentially expressed genes were obtained. To analyze differentially expressed genes in mock treated MDS and HL CD34+ cells we used also the method Significance Analysis of Microarray (SAM). The Delta value was chosen according to number of called genes and percentage of false positive and a log2 fold change threshold >1 was applied. Gene lists were compared by Venn diagrams. Dendrograms were obtained by the software TMEV, MultiExperimentViewer, version 4.0.01. Hierarchical clustering was performed by the association method Average linkage. Annotations of identified genes were obtained on NetAffx Analysis Center (www.affymetrix.com). Differentially expressed genes were then analyzed by GeneOntology to identify the most important biologic processes which were visualized by GO graph.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Francesco,,D'Alò
| | Sample_contact_email | fdalo@rm.unicatt.it
| | Sample_contact_phone | +393497894529
| | Sample_contact_fax | +390635503777
| | Sample_contact_laboratory | Molecular Biology
| | Sample_contact_department | Hematology
| | Sample_contact_institute | Università Cattolica del Sacro Cuore
| | Sample_contact_address | Largo A. Gemelli 8
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM489nnn/GSM489126/suppl/GSM489126.CEL.gz
| | Sample_series_id | GSE19610
| | Sample_data_row_count | 22283
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