Search results for the GEO ID: GSE13284  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM335322 | GPL570 |
|
N1
|
non-targeting siRNA treated erythroid progenitors
|
Control
|
Microarray expression analysis from CD34-derived erythroid progenitors treated with either non-targeting (NT) control siRNAs or BCL11A targeting siRNAs.
|
| Sample_geo_accession | GSM335322
| | Sample_status | Public on Dec 05 2008
| | Sample_submission_date | Oct 20 2008
| | Sample_last_update_date | Nov 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA treated
| | Sample_growth_protocol_ch1 | human cell culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample.
| | Sample_label_ch1 | SAPE
| | Sample_label_protocol_ch1 | The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE
| | Sample_hyb_protocol | The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
| | Sample_scan_protocol | Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
| | Sample_data_processing | dChip normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vijay,G.,Sankaran
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | Children's Hospital Boston
| | Sample_contact_address | 300 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335322/suppl/GSM335322.CEL.gz
| | Sample_series_id | GSE13284
| | Sample_series_id | GSE13285
| | Sample_data_row_count | 54675
| | |
|
GSM335323 | GPL570 |
|
N2
|
non-targeting siRNA treated erythroid progenitors
|
Control
|
Microarray expression analysis from CD34-derived erythroid progenitors treated with either non-targeting (NT) control siRNAs or BCL11A targeting siRNAs.
|
| Sample_geo_accession | GSM335323
| | Sample_status | Public on Dec 05 2008
| | Sample_submission_date | Oct 20 2008
| | Sample_last_update_date | Nov 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA treated
| | Sample_growth_protocol_ch1 | human cell culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample.
| | Sample_label_ch1 | SAPE
| | Sample_label_protocol_ch1 | The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE
| | Sample_hyb_protocol | The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
| | Sample_scan_protocol | Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
| | Sample_data_processing | dChip normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vijay,G.,Sankaran
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | Children's Hospital Boston
| | Sample_contact_address | 300 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335323/suppl/GSM335323.CEL.gz
| | Sample_series_id | GSE13284
| | Sample_series_id | GSE13285
| | Sample_data_row_count | 54675
| | |
|
GSM335324 | GPL570 |
|
N3
|
non-targeting siRNA treated erythroid progenitors
|
Control
|
Microarray expression analysis from CD34-derived erythroid progenitors treated with either non-targeting (NT) control siRNAs or BCL11A targeting siRNAs.
|
| Sample_geo_accession | GSM335324
| | Sample_status | Public on Dec 05 2008
| | Sample_submission_date | Oct 20 2008
| | Sample_last_update_date | Nov 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA treated
| | Sample_growth_protocol_ch1 | human cell culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample.
| | Sample_label_ch1 | SAPE
| | Sample_label_protocol_ch1 | The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE
| | Sample_hyb_protocol | The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
| | Sample_scan_protocol | Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
| | Sample_data_processing | dChip normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vijay,G.,Sankaran
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | Children's Hospital Boston
| | Sample_contact_address | 300 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335324/suppl/GSM335324.CEL.gz
| | Sample_series_id | GSE13284
| | Sample_series_id | GSE13285
| | Sample_data_row_count | 54675
| | |
|
GSM335325 | GPL570 |
|
N4
|
non-targeting siRNA treated erythroid progenitors
|
Control
|
Microarray expression analysis from CD34-derived erythroid progenitors treated with either non-targeting (NT) control siRNAs or BCL11A targeting siRNAs.
|
| Sample_geo_accession | GSM335325
| | Sample_status | Public on Dec 05 2008
| | Sample_submission_date | Oct 20 2008
| | Sample_last_update_date | Nov 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA treated
| | Sample_growth_protocol_ch1 | human cell culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample.
| | Sample_label_ch1 | SAPE
| | Sample_label_protocol_ch1 | The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE
| | Sample_hyb_protocol | The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
| | Sample_scan_protocol | Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
| | Sample_data_processing | dChip normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vijay,G.,Sankaran
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | Children's Hospital Boston
| | Sample_contact_address | 300 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335325/suppl/GSM335325.CEL.gz
| | Sample_series_id | GSE13284
| | Sample_series_id | GSE13285
| | Sample_data_row_count | 54675
| | |
|
GSM335326 | GPL570 |
|
N5
|
non-targeting siRNA treated erythroid progenitors
|
Control
|
Microarray expression analysis from CD34-derived erythroid progenitors treated with either non-targeting (NT) control siRNAs or BCL11A targeting siRNAs.
|
| Sample_geo_accession | GSM335326
| | Sample_status | Public on Dec 05 2008
| | Sample_submission_date | Oct 20 2008
| | Sample_last_update_date | Nov 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA treated
| | Sample_growth_protocol_ch1 | human cell culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample.
| | Sample_label_ch1 | SAPE
| | Sample_label_protocol_ch1 | The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE
| | Sample_hyb_protocol | The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
| | Sample_scan_protocol | Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
| | Sample_data_processing | dChip normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vijay,G.,Sankaran
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | Children's Hospital Boston
| | Sample_contact_address | 300 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335326/suppl/GSM335326.CEL.gz
| | Sample_series_id | GSE13284
| | Sample_series_id | GSE13285
| | Sample_data_row_count | 54675
| | |
|
GSM335327 | GPL570 |
|
N6
|
non-targeting siRNA treated erythroid progenitors
|
Control
|
Microarray expression analysis from CD34-derived erythroid progenitors treated with either non-targeting (NT) control siRNAs or BCL11A targeting siRNAs.
|
| Sample_geo_accession | GSM335327
| | Sample_status | Public on Dec 05 2008
| | Sample_submission_date | Oct 20 2008
| | Sample_last_update_date | Nov 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA treated
| | Sample_growth_protocol_ch1 | human cell culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample.
| | Sample_label_ch1 | SAPE
| | Sample_label_protocol_ch1 | The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE
| | Sample_hyb_protocol | The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
| | Sample_scan_protocol | Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
| | Sample_data_processing | dChip normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vijay,G.,Sankaran
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | Children's Hospital Boston
| | Sample_contact_address | 300 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335327/suppl/GSM335327.CEL.gz
| | Sample_series_id | GSE13284
| | Sample_series_id | GSE13285
| | Sample_data_row_count | 54675
| | |
|
GSM335328 | GPL570 |
|
B1
|
BCL11A siRNA treated erythroid progenitors
|
Gene Knockdown
|
Microarray expression analysis from CD34-derived erythroid progenitors treated with either non-targeting (NT) control siRNAs or BCL11A targeting siRNAs.
|
| Sample_geo_accession | GSM335328
| | Sample_status | Public on Dec 05 2008
| | Sample_submission_date | Oct 20 2008
| | Sample_last_update_date | Nov 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA treated
| | Sample_growth_protocol_ch1 | human cell culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample.
| | Sample_label_ch1 | SAPE
| | Sample_label_protocol_ch1 | The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE
| | Sample_hyb_protocol | The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
| | Sample_scan_protocol | Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
| | Sample_data_processing | dChip normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vijay,G.,Sankaran
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | Children's Hospital Boston
| | Sample_contact_address | 300 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335328/suppl/GSM335328.CEL.gz
| | Sample_series_id | GSE13284
| | Sample_series_id | GSE13285
| | Sample_data_row_count | 54675
| | |
|
GSM335329 | GPL570 |
|
B2
|
BCL11A siRNA treated erythroid progenitors
|
Gene Knockdown
|
Microarray expression analysis from CD34-derived erythroid progenitors treated with either non-targeting (NT) control siRNAs or BCL11A targeting siRNAs.
|
| Sample_geo_accession | GSM335329
| | Sample_status | Public on Dec 05 2008
| | Sample_submission_date | Oct 20 2008
| | Sample_last_update_date | Nov 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA treated
| | Sample_growth_protocol_ch1 | human cell culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample.
| | Sample_label_ch1 | SAPE
| | Sample_label_protocol_ch1 | The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE
| | Sample_hyb_protocol | The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
| | Sample_scan_protocol | Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
| | Sample_data_processing | dChip normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vijay,G.,Sankaran
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | Children's Hospital Boston
| | Sample_contact_address | 300 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335329/suppl/GSM335329.CEL.gz
| | Sample_series_id | GSE13284
| | Sample_series_id | GSE13285
| | Sample_data_row_count | 54675
| | |
|
GSM335330 | GPL570 |
|
B3
|
BCL11A siRNA treated erythroid progenitors
|
Gene Knockdown
|
Microarray expression analysis from CD34-derived erythroid progenitors treated with either non-targeting (NT) control siRNAs or BCL11A targeting siRNAs.
|
| Sample_geo_accession | GSM335330
| | Sample_status | Public on Dec 05 2008
| | Sample_submission_date | Oct 20 2008
| | Sample_last_update_date | Nov 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA treated
| | Sample_growth_protocol_ch1 | human cell culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample.
| | Sample_label_ch1 | SAPE
| | Sample_label_protocol_ch1 | The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE
| | Sample_hyb_protocol | The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
| | Sample_scan_protocol | Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
| | Sample_data_processing | dChip normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vijay,G.,Sankaran
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | Children's Hospital Boston
| | Sample_contact_address | 300 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335330/suppl/GSM335330.CEL.gz
| | Sample_series_id | GSE13284
| | Sample_series_id | GSE13285
| | Sample_data_row_count | 54675
| | |
|
GSM335331 | GPL570 |
|
B4
|
BCL11A siRNA treated erythroid progenitors
|
Gene Knockdown
|
Microarray expression analysis from CD34-derived erythroid progenitors treated with either non-targeting (NT) control siRNAs or BCL11A targeting siRNAs.
|
| Sample_geo_accession | GSM335331
| | Sample_status | Public on Dec 05 2008
| | Sample_submission_date | Oct 20 2008
| | Sample_last_update_date | Nov 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA treated
| | Sample_growth_protocol_ch1 | human cell culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample.
| | Sample_label_ch1 | SAPE
| | Sample_label_protocol_ch1 | The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE
| | Sample_hyb_protocol | The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
| | Sample_scan_protocol | Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
| | Sample_data_processing | dChip normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vijay,G.,Sankaran
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | Children's Hospital Boston
| | Sample_contact_address | 300 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335331/suppl/GSM335331.CEL.gz
| | Sample_series_id | GSE13284
| | Sample_series_id | GSE13285
| | Sample_data_row_count | 54675
| | |
|
GSM335332 | GPL570 |
|
B5
|
BCL11A siRNA treated erythroid progenitors
|
Gene Knockdown
|
Microarray expression analysis from CD34-derived erythroid progenitors treated with either non-targeting (NT) control siRNAs or BCL11A targeting siRNAs.
|
| Sample_geo_accession | GSM335332
| | Sample_status | Public on Dec 05 2008
| | Sample_submission_date | Oct 20 2008
| | Sample_last_update_date | Nov 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA treated
| | Sample_growth_protocol_ch1 | human cell culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample.
| | Sample_label_ch1 | SAPE
| | Sample_label_protocol_ch1 | The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE
| | Sample_hyb_protocol | The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
| | Sample_scan_protocol | Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
| | Sample_data_processing | dChip normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vijay,G.,Sankaran
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | Children's Hospital Boston
| | Sample_contact_address | 300 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335332/suppl/GSM335332.CEL.gz
| | Sample_series_id | GSE13284
| | Sample_series_id | GSE13285
| | Sample_data_row_count | 54675
| | |
|
GSM335333 | GPL570 |
|
B6
|
BCL11A siRNA treated erythroid progenitors
|
Gene Knockdown
|
Microarray expression analysis from CD34-derived erythroid progenitors treated with either non-targeting (NT) control siRNAs or BCL11A targeting siRNAs.
|
| Sample_geo_accession | GSM335333
| | Sample_status | Public on Dec 05 2008
| | Sample_submission_date | Oct 20 2008
| | Sample_last_update_date | Nov 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA treated
| | Sample_growth_protocol_ch1 | human cell culture
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample.
| | Sample_label_ch1 | SAPE
| | Sample_label_protocol_ch1 | The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE
| | Sample_hyb_protocol | The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
| | Sample_scan_protocol | Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
| | Sample_data_processing | dChip normalization
| | Sample_platform_id | GPL570
| | Sample_contact_name | Vijay,G.,Sankaran
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | Children's Hospital Boston
| | Sample_contact_address | 300 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335333/suppl/GSM335333.CEL.gz
| | Sample_series_id | GSE13284
| | Sample_series_id | GSE13285
| | Sample_data_row_count | 54675
| | |
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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