Search results for the GEO ID: GSE30585  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM758764 | GPL570 |
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of CID, biological replicate 1
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of CID
|
cell type: CD34+GFP+ cells isolated form culture on day 7
genotype/variation: F36VMpl transduced
|
Gene expression data from F36VMpl transduced cord blood CD34+ cells cultured in the presence of CID
|
| Sample_geo_accession | GSM758764
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Jul 12 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_growth_protocol_ch1 | CB CD34+ cells transduced with F36VMpl-GFP were cultured on MS-5 stroma in lymphoid medium (RPMI 1640 [Irvine Scientific, Santa Ana, CA], 5% FCS [screened for B-cell cultures], 50 mM 2-ME, 50 U/mL penicillin/50 microgram/mL streptomycin,and 200 mM L-glutamie), either with CID alone, with Epo(5 international units/ ml) alone, or with Tpo (50 ng/ ml) alone. Transduced cells cultured on MS-5 stroma in the absence of either growth factors or CID served as controls. Three biologically independent experiments were performed. CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a Qiagen micro kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Total RNA (1 μg to 15 μg) was first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and used as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45 degree celcius for 16 hours.They were then washed and stained with a streptavidin phycoerythrin conjugate
| | Sample_scan_protocol | GeneChip Scanner 3000DX V.2
| | Sample_data_processing | dCHIP software (Department of biostatistics, Harvard School of Public Health, Boston, MA). The quantile method was used to normalize gene expression values in a PM/MM model. Gene expression values from the sample NCID2 served as a baseline for normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | chintan,,parekh
| | Sample_contact_email | cparekh@mednet.ucla.edu
| | Sample_contact_laboratory | Crooks
| | Sample_contact_department | Pathology
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 610 Charles Young Drive
| | Sample_contact_city | Los Angeles
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM758nnn/GSM758764/suppl/GSM758764.CEL.gz
| | Sample_series_id | GSE30585
| | Sample_data_row_count | 54675
| | |
|
GSM758765 | GPL570 |
|
F36VMpl transduced cord blood CD34+ cells cultured in the absence of CID or growth factors, biological replicate 1
|
F36VMpl transduced cord blood CD34+ cells cultured in the absence of CID or growth factors
|
cell type: CD34+GFP+ cells isolated form culture on day 7
genotype/variation: F36VMpl transduced
|
Gene expression data from F36VMpl transduced cord blood CD34+ cells cultured in the absence of CID or growth factors
|
| Sample_geo_accession | GSM758765
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Jul 12 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_growth_protocol_ch1 | CB CD34+ cells transduced with F36VMpl-GFP were cultured on MS-5 stroma in lymphoid medium (RPMI 1640 [Irvine Scientific, Santa Ana, CA], 5% FCS [screened for B-cell cultures], 50 mM 2-ME, 50 U/mL penicillin/50 microgram/mL streptomycin,and 200 mM L-glutamie), either with CID alone, with Epo(5 international units/ ml) alone, or with Tpo (50 ng/ ml) alone. Transduced cells cultured on MS-5 stroma in the absence of either growth factors or CID served as controls. Three biologically independent experiments were performed. CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a Qiagen micro kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Total RNA (1 μg to 15 μg) was first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and used as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45 degree celcius for 16 hours.They were then washed and stained with a streptavidin phycoerythrin conjugate
| | Sample_scan_protocol | GeneChip Scanner 3000DX V.2
| | Sample_data_processing | dCHIP software (Department of biostatistics, Harvard School of Public Health, Boston, MA). The quantile method was used to normalize gene expression values in a PM/MM model. Gene expression values from the sample NCID2 served as a baseline for normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | chintan,,parekh
| | Sample_contact_email | cparekh@mednet.ucla.edu
| | Sample_contact_laboratory | Crooks
| | Sample_contact_department | Pathology
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 610 Charles Young Drive
| | Sample_contact_city | Los Angeles
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM758nnn/GSM758765/suppl/GSM758765.CEL.gz
| | Sample_series_id | GSE30585
| | Sample_data_row_count | 54675
| | |
|
GSM758766 | GPL570 |
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of Tpo, biological replicate 1
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of Tpo
|
cell type: CD34+GFP+ cells isolated form culture on day 7
genotype/variation: F36VMpl transduced
|
Gene expression data from F36VMpl transduced cord blood CD34+ cells cultured in the presence of Tpo
|
| Sample_geo_accession | GSM758766
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Jul 12 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_growth_protocol_ch1 | CB CD34+ cells transduced with F36VMpl-GFP were cultured on MS-5 stroma in lymphoid medium (RPMI 1640 [Irvine Scientific, Santa Ana, CA], 5% FCS [screened for B-cell cultures], 50 mM 2-ME, 50 U/mL penicillin/50 microgram/mL streptomycin,and 200 mM L-glutamie), either with CID alone, with Epo(5 international units/ ml) alone, or with Tpo (50 ng/ ml) alone. Transduced cells cultured on MS-5 stroma in the absence of either growth factors or CID served as controls. Three biologically independent experiments were performed. CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a Qiagen micro kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Total RNA (1 μg to 15 μg) was first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and used as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45 degree celcius for 16 hours.They were then washed and stained with a streptavidin phycoerythrin conjugate
| | Sample_scan_protocol | GeneChip Scanner 3000DX V.2
| | Sample_data_processing | dCHIP software (Department of biostatistics, Harvard School of Public Health, Boston, MA). The quantile method was used to normalize gene expression values in a PM/MM model. Gene expression values from the sample NCID2 served as a baseline for normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | chintan,,parekh
| | Sample_contact_email | cparekh@mednet.ucla.edu
| | Sample_contact_laboratory | Crooks
| | Sample_contact_department | Pathology
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 610 Charles Young Drive
| | Sample_contact_city | Los Angeles
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM758nnn/GSM758766/suppl/GSM758766.CEL.gz
| | Sample_series_id | GSE30585
| | Sample_data_row_count | 54675
| | |
|
GSM758767 | GPL570 |
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of Epo, biological replicate 1
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of Epo
|
cell type: CD34+GFP+ cells isolated form culture on day 7
genotype/variation: F36VMpl transduced
|
Gene expression data from F36VMpl transduced cord blood CD34+ cells cultured in the presence of Epo
|
| Sample_geo_accession | GSM758767
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Jul 12 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_growth_protocol_ch1 | CB CD34+ cells transduced with F36VMpl-GFP were cultured on MS-5 stroma in lymphoid medium (RPMI 1640 [Irvine Scientific, Santa Ana, CA], 5% FCS [screened for B-cell cultures], 50 mM 2-ME, 50 U/mL penicillin/50 microgram/mL streptomycin,and 200 mM L-glutamie), either with CID alone, with Epo(5 international units/ ml) alone, or with Tpo (50 ng/ ml) alone. Transduced cells cultured on MS-5 stroma in the absence of either growth factors or CID served as controls. Three biologically independent experiments were performed. CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a Qiagen micro kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Total RNA (1 μg to 15 μg) was first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and used as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45 degree celcius for 16 hours.They were then washed and stained with a streptavidin phycoerythrin conjugate
| | Sample_scan_protocol | GeneChip Scanner 3000DX V.2
| | Sample_data_processing | dCHIP software (Department of biostatistics, Harvard School of Public Health, Boston, MA). The quantile method was used to normalize gene expression values in a PM/MM model. Gene expression values from the sample NCID2 served as a baseline for normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | chintan,,parekh
| | Sample_contact_email | cparekh@mednet.ucla.edu
| | Sample_contact_laboratory | Crooks
| | Sample_contact_department | Pathology
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 610 Charles Young Drive
| | Sample_contact_city | Los Angeles
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM758nnn/GSM758767/suppl/GSM758767.CEL.gz
| | Sample_series_id | GSE30585
| | Sample_data_row_count | 54675
| | |
|
GSM758768 | GPL570 |
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of CID, biological replicate 2
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of CID
|
cell type: CD34+GFP+ cells isolated form culture on day 7
genotype/variation: F36VMpl transduced
|
Gene expression data from F36VMpl transduced cord blood CD34+ cells cultured in the presence of CID
|
| Sample_geo_accession | GSM758768
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Jul 12 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_growth_protocol_ch1 | CB CD34+ cells transduced with F36VMpl-GFP were cultured on MS-5 stroma in lymphoid medium (RPMI 1640 [Irvine Scientific, Santa Ana, CA], 5% FCS [screened for B-cell cultures], 50 mM 2-ME, 50 U/mL penicillin/50 microgram/mL streptomycin,and 200 mM L-glutamie), either with CID alone, with Epo(5 international units/ ml) alone, or with Tpo (50 ng/ ml) alone. Transduced cells cultured on MS-5 stroma in the absence of either growth factors or CID served as controls. Three biologically independent experiments were performed. CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a Qiagen micro kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Total RNA (1 μg to 15 μg) was first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and used as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45 degree celcius for 16 hours.They were then washed and stained with a streptavidin phycoerythrin conjugate
| | Sample_scan_protocol | GeneChip Scanner 3000DX V.2
| | Sample_data_processing | dCHIP software (Department of biostatistics, Harvard School of Public Health, Boston, MA). The quantile method was used to normalize gene expression values in a PM/MM model. Gene expression values from the sample NCID2 served as a baseline for normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | chintan,,parekh
| | Sample_contact_email | cparekh@mednet.ucla.edu
| | Sample_contact_laboratory | Crooks
| | Sample_contact_department | Pathology
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 610 Charles Young Drive
| | Sample_contact_city | Los Angeles
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM758nnn/GSM758768/suppl/GSM758768.CEL.gz
| | Sample_series_id | GSE30585
| | Sample_data_row_count | 54675
| | |
|
GSM758769 | GPL570 |
|
F36VMpl transduced cord blood CD34+ cells cultured in the absence of CID or growth factors, biological replicate 2
|
F36VMpl transduced cord blood CD34+ cells cultured in the absence of CID or growth factors
|
cell type: CD34+GFP+ cells isolated form culture on day 7
genotype/variation: F36VMpl transduced
|
Gene expression data from F36VMpl transduced cord blood CD34+ cells cultured in the absence of CID or growth factors
|
| Sample_geo_accession | GSM758769
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Jul 12 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_growth_protocol_ch1 | CB CD34+ cells transduced with F36VMpl-GFP were cultured on MS-5 stroma in lymphoid medium (RPMI 1640 [Irvine Scientific, Santa Ana, CA], 5% FCS [screened for B-cell cultures], 50 mM 2-ME, 50 U/mL penicillin/50 microgram/mL streptomycin,and 200 mM L-glutamie), either with CID alone, with Epo(5 international units/ ml) alone, or with Tpo (50 ng/ ml) alone. Transduced cells cultured on MS-5 stroma in the absence of either growth factors or CID served as controls. Three biologically independent experiments were performed. CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a Qiagen micro kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Total RNA (1 μg to 15 μg) was first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and used as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45 degree celcius for 16 hours.They were then washed and stained with a streptavidin phycoerythrin conjugate
| | Sample_scan_protocol | GeneChip Scanner 3000DX V.2
| | Sample_data_processing | dCHIP software (Department of biostatistics, Harvard School of Public Health, Boston, MA). The quantile method was used to normalize gene expression values in a PM/MM model. Gene expression values from the sample NCID2 served as a baseline for normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | chintan,,parekh
| | Sample_contact_email | cparekh@mednet.ucla.edu
| | Sample_contact_laboratory | Crooks
| | Sample_contact_department | Pathology
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 610 Charles Young Drive
| | Sample_contact_city | Los Angeles
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM758nnn/GSM758769/suppl/GSM758769.CEL.gz
| | Sample_series_id | GSE30585
| | Sample_data_row_count | 54675
| | |
|
GSM758770 | GPL570 |
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of Tpo, biological replicate 2
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of Tpo
|
cell type: CD34+GFP+ cells isolated form culture on day 7
genotype/variation: F36VMpl transduced
|
Gene expression data from F36VMpl transduced cord blood CD34+ cells cultured in the presence of Tpo
|
| Sample_geo_accession | GSM758770
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Jul 12 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_growth_protocol_ch1 | CB CD34+ cells transduced with F36VMpl-GFP were cultured on MS-5 stroma in lymphoid medium (RPMI 1640 [Irvine Scientific, Santa Ana, CA], 5% FCS [screened for B-cell cultures], 50 mM 2-ME, 50 U/mL penicillin/50 microgram/mL streptomycin,and 200 mM L-glutamie), either with CID alone, with Epo(5 international units/ ml) alone, or with Tpo (50 ng/ ml) alone. Transduced cells cultured on MS-5 stroma in the absence of either growth factors or CID served as controls. Three biologically independent experiments were performed. CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a Qiagen micro kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Total RNA (1 μg to 15 μg) was first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and used as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45 degree celcius for 16 hours.They were then washed and stained with a streptavidin phycoerythrin conjugate
| | Sample_scan_protocol | GeneChip Scanner 3000DX V.2
| | Sample_data_processing | dCHIP software (Department of biostatistics, Harvard School of Public Health, Boston, MA). The quantile method was used to normalize gene expression values in a PM/MM model. Gene expression values from the sample NCID2 served as a baseline for normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | chintan,,parekh
| | Sample_contact_email | cparekh@mednet.ucla.edu
| | Sample_contact_laboratory | Crooks
| | Sample_contact_department | Pathology
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 610 Charles Young Drive
| | Sample_contact_city | Los Angeles
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM758nnn/GSM758770/suppl/GSM758770.CEL.gz
| | Sample_series_id | GSE30585
| | Sample_data_row_count | 54675
| | |
|
GSM758771 | GPL570 |
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of Epo, biological replicate 2
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of Epo
|
cell type: CD34+GFP+ cells isolated form culture on day 7
genotype/variation: F36VMpl transduced
|
Gene expression data from F36VMpl transduced cord blood CD34+ cells cultured in the presence of Epo
|
| Sample_geo_accession | GSM758771
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Jul 12 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_growth_protocol_ch1 | CB CD34+ cells transduced with F36VMpl-GFP were cultured on MS-5 stroma in lymphoid medium (RPMI 1640 [Irvine Scientific, Santa Ana, CA], 5% FCS [screened for B-cell cultures], 50 mM 2-ME, 50 U/mL penicillin/50 microgram/mL streptomycin,and 200 mM L-glutamie), either with CID alone, with Epo(5 international units/ ml) alone, or with Tpo (50 ng/ ml) alone. Transduced cells cultured on MS-5 stroma in the absence of either growth factors or CID served as controls. Three biologically independent experiments were performed. CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a Qiagen micro kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Total RNA (1 μg to 15 μg) was first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and used as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45 degree celcius for 16 hours.They were then washed and stained with a streptavidin phycoerythrin conjugate
| | Sample_scan_protocol | GeneChip Scanner 3000DX V.2
| | Sample_data_processing | dCHIP software (Department of biostatistics, Harvard School of Public Health, Boston, MA). The quantile method was used to normalize gene expression values in a PM/MM model. Gene expression values from the sample NCID2 served as a baseline for normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | chintan,,parekh
| | Sample_contact_email | cparekh@mednet.ucla.edu
| | Sample_contact_laboratory | Crooks
| | Sample_contact_department | Pathology
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 610 Charles Young Drive
| | Sample_contact_city | Los Angeles
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM758nnn/GSM758771/suppl/GSM758771.CEL.gz
| | Sample_series_id | GSE30585
| | Sample_data_row_count | 54675
| | |
|
GSM758772 | GPL570 |
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of CID, biological replicate 3
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of CID
|
cell type: CD34+GFP+ cells isolated form culture on day 7
genotype/variation: F36VMpl transduced
|
Gene expression data from F36VMpl transduced cord blood CD34+ cells cultured in the presence of CID
|
| Sample_geo_accession | GSM758772
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Jul 12 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_growth_protocol_ch1 | CB CD34+ cells transduced with F36VMpl-GFP were cultured on MS-5 stroma in lymphoid medium (RPMI 1640 [Irvine Scientific, Santa Ana, CA], 5% FCS [screened for B-cell cultures], 50 mM 2-ME, 50 U/mL penicillin/50 microgram/mL streptomycin,and 200 mM L-glutamie), either with CID alone, with Epo(5 international units/ ml) alone, or with Tpo (50 ng/ ml) alone. Transduced cells cultured on MS-5 stroma in the absence of either growth factors or CID served as controls. Three biologically independent experiments were performed. CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a Qiagen micro kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Total RNA (1 μg to 15 μg) was first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and used as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45 degree celcius for 16 hours.They were then washed and stained with a streptavidin phycoerythrin conjugate
| | Sample_scan_protocol | GeneChip Scanner 3000DX V.2
| | Sample_data_processing | dCHIP software (Department of biostatistics, Harvard School of Public Health, Boston, MA). The quantile method was used to normalize gene expression values in a PM/MM model. Gene expression values from the sample NCID2 served as a baseline for normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | chintan,,parekh
| | Sample_contact_email | cparekh@mednet.ucla.edu
| | Sample_contact_laboratory | Crooks
| | Sample_contact_department | Pathology
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 610 Charles Young Drive
| | Sample_contact_city | Los Angeles
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM758nnn/GSM758772/suppl/GSM758772.CEL.gz
| | Sample_series_id | GSE30585
| | Sample_data_row_count | 54675
| | |
|
GSM758773 | GPL570 |
|
F36VMpl transduced cord blood CD34+ cells cultured in the absence of CID or growth factors, biological replicate 3
|
F36VMpl transduced cord blood CD34+ cells cultured in the absence of CID or growth factors
|
cell type: CD34+GFP+ cells isolated form culture on day 7
genotype/variation: F36VMpl transduced
|
Gene expression data from F36VMpl transduced cord blood CD34+ cells cultured in the absence of CID or growth factors
|
| Sample_geo_accession | GSM758773
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Jul 12 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_growth_protocol_ch1 | CB CD34+ cells transduced with F36VMpl-GFP were cultured on MS-5 stroma in lymphoid medium (RPMI 1640 [Irvine Scientific, Santa Ana, CA], 5% FCS [screened for B-cell cultures], 50 mM 2-ME, 50 U/mL penicillin/50 microgram/mL streptomycin,and 200 mM L-glutamie), either with CID alone, with Epo(5 international units/ ml) alone, or with Tpo (50 ng/ ml) alone. Transduced cells cultured on MS-5 stroma in the absence of either growth factors or CID served as controls. Three biologically independent experiments were performed. CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a Qiagen micro kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Total RNA (1 μg to 15 μg) was first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and used as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45 degree celcius for 16 hours.They were then washed and stained with a streptavidin phycoerythrin conjugate
| | Sample_scan_protocol | GeneChip Scanner 3000DX V.2
| | Sample_data_processing | dCHIP software (Department of biostatistics, Harvard School of Public Health, Boston, MA). The quantile method was used to normalize gene expression values in a PM/MM model. Gene expression values from the sample NCID2 served as a baseline for normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | chintan,,parekh
| | Sample_contact_email | cparekh@mednet.ucla.edu
| | Sample_contact_laboratory | Crooks
| | Sample_contact_department | Pathology
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 610 Charles Young Drive
| | Sample_contact_city | Los Angeles
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM758nnn/GSM758773/suppl/GSM758773.CEL.gz
| | Sample_series_id | GSE30585
| | Sample_data_row_count | 54675
| | |
|
GSM758774 | GPL570 |
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of Tpo, biological replicate 3
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of Tpo
|
cell type: CD34+GFP+ cells isolated form culture on day 7
genotype/variation: F36VMpl transduced
|
Gene expression data from F36VMpl transduced cord blood CD34+ cells cultured in the presence of Tpo
|
| Sample_geo_accession | GSM758774
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Jul 12 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_growth_protocol_ch1 | CB CD34+ cells transduced with F36VMpl-GFP were cultured on MS-5 stroma in lymphoid medium (RPMI 1640 [Irvine Scientific, Santa Ana, CA], 5% FCS [screened for B-cell cultures], 50 mM 2-ME, 50 U/mL penicillin/50 microgram/mL streptomycin,and 200 mM L-glutamie), either with CID alone, with Epo(5 international units/ ml) alone, or with Tpo (50 ng/ ml) alone. Transduced cells cultured on MS-5 stroma in the absence of either growth factors or CID served as controls. Three biologically independent experiments were performed. CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a Qiagen micro kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Total RNA (1 μg to 15 μg) was first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and used as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45 degree celcius for 16 hours.They were then washed and stained with a streptavidin phycoerythrin conjugate
| | Sample_scan_protocol | GeneChip Scanner 3000DX V.2
| | Sample_data_processing | dCHIP software (Department of biostatistics, Harvard School of Public Health, Boston, MA). The quantile method was used to normalize gene expression values in a PM/MM model. Gene expression values from the sample NCID2 served as a baseline for normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | chintan,,parekh
| | Sample_contact_email | cparekh@mednet.ucla.edu
| | Sample_contact_laboratory | Crooks
| | Sample_contact_department | Pathology
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 610 Charles Young Drive
| | Sample_contact_city | Los Angeles
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM758nnn/GSM758774/suppl/GSM758774.CEL.gz
| | Sample_series_id | GSE30585
| | Sample_data_row_count | 54675
| | |
|
GSM758775 | GPL570 |
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of Epo, biological replicate 3
|
F36VMpl transduced cord blood CD34+ cells cultured in the presence of Epo
|
cell type: CD34+GFP+ cells isolated form culture on day 7
genotype/variation: F36VMpl transduced
|
Gene expression data from F36VMpl transduced cord blood CD34+ cells cultured in the presence of Epo
|
| Sample_geo_accession | GSM758775
| | Sample_status | Public on Sep 01 2011
| | Sample_submission_date | Jul 12 2011
| | Sample_last_update_date | Sep 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_growth_protocol_ch1 | CB CD34+ cells transduced with F36VMpl-GFP were cultured on MS-5 stroma in lymphoid medium (RPMI 1640 [Irvine Scientific, Santa Ana, CA], 5% FCS [screened for B-cell cultures], 50 mM 2-ME, 50 U/mL penicillin/50 microgram/mL streptomycin,and 200 mM L-glutamie), either with CID alone, with Epo(5 international units/ ml) alone, or with Tpo (50 ng/ ml) alone. Transduced cells cultured on MS-5 stroma in the absence of either growth factors or CID served as controls. Three biologically independent experiments were performed. CD34+GFP+ cells were isolated by FACS after 7days of culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using a Qiagen micro kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Total RNA (1 μg to 15 μg) was first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and used as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45 degree celcius for 16 hours.They were then washed and stained with a streptavidin phycoerythrin conjugate
| | Sample_scan_protocol | GeneChip Scanner 3000DX V.2
| | Sample_data_processing | dCHIP software (Department of biostatistics, Harvard School of Public Health, Boston, MA). The quantile method was used to normalize gene expression values in a PM/MM model. Gene expression values from the sample NCID2 served as a baseline for normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | chintan,,parekh
| | Sample_contact_email | cparekh@mednet.ucla.edu
| | Sample_contact_laboratory | Crooks
| | Sample_contact_department | Pathology
| | Sample_contact_institute | UCLA
| | Sample_contact_address | 610 Charles Young Drive
| | Sample_contact_city | Los Angeles
| | Sample_contact_zip/postal_code | 90095
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM758nnn/GSM758775/suppl/GSM758775.CEL.gz
| | Sample_series_id | GSE30585
| | Sample_data_row_count | 54675
| | |
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