Search results for the GEO ID: GSE30318  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM751543 | GPL1261 |
|
wild-type_no TNF_rep1
|
c-Kit+Sca-1+Lin- bone marrow cells from wild-type mouse, cultured in growth factors alone
|
genotype/variation: wild-type
age: 2-4 months
cell type: hematopoietic progenitor cells
|
|
| Sample_geo_accession | GSM751543
| | Sample_status | Public on May 23 2012
| | Sample_submission_date | Jun 30 2011
| | Sample_last_update_date | May 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Immediately after plating cells, half of the samples were treated with 10 ng/ml TNF alpha for 24 hours before RNA harvest. The other half of the samples received medium alone.
| | Sample_growth_protocol_ch1 | Freshly-isolated KSL cells were placed into culture dishes at a density of 104 per ml medium. Medium was RPMI containing 10% fetal bovine serum, 20 ng/ml IL-6, 10 ng/ml IL-11, 50 ng/ml Flt3L, and 10 ng/ml SCF.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected from medium by centrifugation, lysed with 75 ul QIAGEN RLT buffer, then RNA extracted with the QIAGEN Rneasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to amplified cDNA using the NuGEN Ovation RNA amplification v.2 System. Using between 5-15ng of total RNA as input, in a three step process, total RNA was converted to cDNA: (1) First Strand Synthesis: Single stranded cDNA was prepared from total RNA using a chimeric DNA/RNA primers and reverse transcriptase, (Step 2) Second Strand Synthesis: After partial fragmentation of mRNA in the cDNA/mRNA complex, DNA polymerase generated a second strand, (3) SPIA Amplification: The isothermal linear amplification step used an additional DNA/RNA chimeric primer, DNA polymerase and RNase H in an isothermal reaction creating antisense strand cDNA The cDNA was fragmented to produce a uniform distribution of short cDNAs and biotin labeled using the NuGEN Ovation FLv2 reagents. 3.4µg each of labeled target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.
| | Sample_hyb_protocol | The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 18 hours at 45 degrees C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 450s (Affymetrix, Santa Clara, CA) using the FS450_0004 Affymetrix fluidics script. Hybridization date: 01/28/08; Array lot: 4035270
| | Sample_scan_protocol | The distribution of fluorescent material on the processed array was determined using the Affymetrix GS300 Scanner with the 7G upgrade. The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.
| | Sample_data_processing | The data were processed by GeneSifter software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Grover,C,Bagby, MD
| | Sample_contact_email | grover@ohsu.edu
| | Sample_contact_laboratory | Knight Cancer Institute
| | Sample_contact_department | Dept. of Medicine
| | Sample_contact_institute | Oregon Health & Science University
| | Sample_contact_address | 3181 SW Sam Jackson Park Rd.
| | Sample_contact_city | Portland
| | Sample_contact_state | OR
| | Sample_contact_zip/postal_code | 97239
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM751nnn/GSM751543/suppl/GSM751543.CEL.gz
| | Sample_series_id | GSE30318
| | Sample_data_row_count | 45101
| | |
|
GSM751544 | GPL1261 |
|
wild-type_no TNF_rep2
|
c-Kit+Sca-1+Lin- bone marrow cells from wild-type mouse, cultured in growth factors alone
|
genotype/variation: wild-type
age: 2-4 months
cell type: hematopoietic progenitor cells
|
|
| Sample_geo_accession | GSM751544
| | Sample_status | Public on May 23 2012
| | Sample_submission_date | Jun 30 2011
| | Sample_last_update_date | May 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Immediately after plating cells, half of the samples were treated with 10 ng/ml TNF alpha for 24 hours before RNA harvest. The other half of the samples received medium alone.
| | Sample_growth_protocol_ch1 | Freshly-isolated KSL cells were placed into culture dishes at a density of 104 per ml medium. Medium was RPMI containing 10% fetal bovine serum, 20 ng/ml IL-6, 10 ng/ml IL-11, 50 ng/ml Flt3L, and 10 ng/ml SCF.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected from medium by centrifugation, lysed with 75 ul QIAGEN RLT buffer, then RNA extracted with the QIAGEN Rneasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to amplified cDNA using the NuGEN Ovation RNA amplification v.2 System. Using between 5-15ng of total RNA as input, in a three step process, total RNA was converted to cDNA: (1) First Strand Synthesis: Single stranded cDNA was prepared from total RNA using a chimeric DNA/RNA primers and reverse transcriptase, (Step 2) Second Strand Synthesis: After partial fragmentation of mRNA in the cDNA/mRNA complex, DNA polymerase generated a second strand, (3) SPIA Amplification: The isothermal linear amplification step used an additional DNA/RNA chimeric primer, DNA polymerase and RNase H in an isothermal reaction creating antisense strand cDNA The cDNA was fragmented to produce a uniform distribution of short cDNAs and biotin labeled using the NuGEN Ovation FLv2 reagents. 3.4µg each of labeled target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.
| | Sample_hyb_protocol | The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 18 hours at 45 degrees C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 450s (Affymetrix, Santa Clara, CA) using the FS450_0004 Affymetrix fluidics script. Hybridization date: 01/28/08; Array lot: 4035270
| | Sample_scan_protocol | The distribution of fluorescent material on the processed array was determined using the Affymetrix GS300 Scanner with the 7G upgrade. The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.
| | Sample_data_processing | The data were processed by GeneSifter software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Grover,C,Bagby, MD
| | Sample_contact_email | grover@ohsu.edu
| | Sample_contact_laboratory | Knight Cancer Institute
| | Sample_contact_department | Dept. of Medicine
| | Sample_contact_institute | Oregon Health & Science University
| | Sample_contact_address | 3181 SW Sam Jackson Park Rd.
| | Sample_contact_city | Portland
| | Sample_contact_state | OR
| | Sample_contact_zip/postal_code | 97239
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM751nnn/GSM751544/suppl/GSM751544.CEL.gz
| | Sample_series_id | GSE30318
| | Sample_data_row_count | 45101
| | |
|
GSM751545 | GPL1261 |
|
wild-type_no TNF_rep3
|
c-Kit+Sca-1+Lin- bone marrow cells from wild-type mouse, cultured in growth factors alone
|
genotype/variation: wild-type
age: 2-4 months
cell type: hematopoietic progenitor cells
|
|
| Sample_geo_accession | GSM751545
| | Sample_status | Public on May 23 2012
| | Sample_submission_date | Jun 30 2011
| | Sample_last_update_date | May 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Immediately after plating cells, half of the samples were treated with 10 ng/ml TNF alpha for 24 hours before RNA harvest. The other half of the samples received medium alone.
| | Sample_growth_protocol_ch1 | Freshly-isolated KSL cells were placed into culture dishes at a density of 104 per ml medium. Medium was RPMI containing 10% fetal bovine serum, 20 ng/ml IL-6, 10 ng/ml IL-11, 50 ng/ml Flt3L, and 10 ng/ml SCF.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected from medium by centrifugation, lysed with 75 ul QIAGEN RLT buffer, then RNA extracted with the QIAGEN Rneasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to amplified cDNA using the NuGEN Ovation RNA amplification v.2 System. Using between 5-15ng of total RNA as input, in a three step process, total RNA was converted to cDNA: (1) First Strand Synthesis: Single stranded cDNA was prepared from total RNA using a chimeric DNA/RNA primers and reverse transcriptase, (Step 2) Second Strand Synthesis: After partial fragmentation of mRNA in the cDNA/mRNA complex, DNA polymerase generated a second strand, (3) SPIA Amplification: The isothermal linear amplification step used an additional DNA/RNA chimeric primer, DNA polymerase and RNase H in an isothermal reaction creating antisense strand cDNA The cDNA was fragmented to produce a uniform distribution of short cDNAs and biotin labeled using the NuGEN Ovation FLv2 reagents. 3.4µg each of labeled target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.
| | Sample_hyb_protocol | The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 18 hours at 45 degrees C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 450s (Affymetrix, Santa Clara, CA) using the FS450_0004 Affymetrix fluidics script. Hybridization date: 01/28/08; Array lot: 4035270
| | Sample_scan_protocol | The distribution of fluorescent material on the processed array was determined using the Affymetrix GS300 Scanner with the 7G upgrade. The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.
| | Sample_data_processing | The data were processed by GeneSifter software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Grover,C,Bagby, MD
| | Sample_contact_email | grover@ohsu.edu
| | Sample_contact_laboratory | Knight Cancer Institute
| | Sample_contact_department | Dept. of Medicine
| | Sample_contact_institute | Oregon Health & Science University
| | Sample_contact_address | 3181 SW Sam Jackson Park Rd.
| | Sample_contact_city | Portland
| | Sample_contact_state | OR
| | Sample_contact_zip/postal_code | 97239
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM751nnn/GSM751545/suppl/GSM751545.CEL.gz
| | Sample_series_id | GSE30318
| | Sample_data_row_count | 45101
| | |
|
GSM751546 | GPL1261 |
|
mutant_no TNF_rep1
|
c-Kit+Sca-1+Lin- bone marrow cells from Fancc mutant mouse, cultured in growth factors alone
|
genotype/variation: Fancc-/-
age: 2-4 months
cell type: hematopoietic progenitor cells
|
|
| Sample_geo_accession | GSM751546
| | Sample_status | Public on May 23 2012
| | Sample_submission_date | Jun 30 2011
| | Sample_last_update_date | May 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Immediately after plating cells, half of the samples were treated with 10 ng/ml TNF alpha for 24 hours before RNA harvest. The other half of the samples received medium alone.
| | Sample_growth_protocol_ch1 | Freshly-isolated KSL cells were placed into culture dishes at a density of 104 per ml medium. Medium was RPMI containing 10% fetal bovine serum, 20 ng/ml IL-6, 10 ng/ml IL-11, 50 ng/ml Flt3L, and 10 ng/ml SCF.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected from medium by centrifugation, lysed with 75 ul QIAGEN RLT buffer, then RNA extracted with the QIAGEN Rneasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to amplified cDNA using the NuGEN Ovation RNA amplification v.2 System. Using between 5-15ng of total RNA as input, in a three step process, total RNA was converted to cDNA: (1) First Strand Synthesis: Single stranded cDNA was prepared from total RNA using a chimeric DNA/RNA primers and reverse transcriptase, (Step 2) Second Strand Synthesis: After partial fragmentation of mRNA in the cDNA/mRNA complex, DNA polymerase generated a second strand, (3) SPIA Amplification: The isothermal linear amplification step used an additional DNA/RNA chimeric primer, DNA polymerase and RNase H in an isothermal reaction creating antisense strand cDNA The cDNA was fragmented to produce a uniform distribution of short cDNAs and biotin labeled using the NuGEN Ovation FLv2 reagents. 3.4µg each of labeled target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.
| | Sample_hyb_protocol | The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 18 hours at 45 degrees C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 450s (Affymetrix, Santa Clara, CA) using the FS450_0004 Affymetrix fluidics script. Hybridization date: 01/28/08; Array lot: 4035270
| | Sample_scan_protocol | The distribution of fluorescent material on the processed array was determined using the Affymetrix GS300 Scanner with the 7G upgrade. The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.
| | Sample_data_processing | The data were processed by GeneSifter software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Grover,C,Bagby, MD
| | Sample_contact_email | grover@ohsu.edu
| | Sample_contact_laboratory | Knight Cancer Institute
| | Sample_contact_department | Dept. of Medicine
| | Sample_contact_institute | Oregon Health & Science University
| | Sample_contact_address | 3181 SW Sam Jackson Park Rd.
| | Sample_contact_city | Portland
| | Sample_contact_state | OR
| | Sample_contact_zip/postal_code | 97239
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM751nnn/GSM751546/suppl/GSM751546.CEL.gz
| | Sample_series_id | GSE30318
| | Sample_data_row_count | 45101
| | |
|
GSM751547 | GPL1261 |
|
mutant_no TNF_rep2
|
c-Kit+Sca-1+Lin- bone marrow cells from Fancc mutant mouse, cultured in growth factors alone
|
genotype/variation: Fancc-/-
age: 2-4 months
cell type: hematopoietic progenitor cells
|
|
| Sample_geo_accession | GSM751547
| | Sample_status | Public on May 23 2012
| | Sample_submission_date | Jun 30 2011
| | Sample_last_update_date | May 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Immediately after plating cells, half of the samples were treated with 10 ng/ml TNF alpha for 24 hours before RNA harvest. The other half of the samples received medium alone.
| | Sample_growth_protocol_ch1 | Freshly-isolated KSL cells were placed into culture dishes at a density of 104 per ml medium. Medium was RPMI containing 10% fetal bovine serum, 20 ng/ml IL-6, 10 ng/ml IL-11, 50 ng/ml Flt3L, and 10 ng/ml SCF.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected from medium by centrifugation, lysed with 75 ul QIAGEN RLT buffer, then RNA extracted with the QIAGEN Rneasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to amplified cDNA using the NuGEN Ovation RNA amplification v.2 System. Using between 5-15ng of total RNA as input, in a three step process, total RNA was converted to cDNA: (1) First Strand Synthesis: Single stranded cDNA was prepared from total RNA using a chimeric DNA/RNA primers and reverse transcriptase, (Step 2) Second Strand Synthesis: After partial fragmentation of mRNA in the cDNA/mRNA complex, DNA polymerase generated a second strand, (3) SPIA Amplification: The isothermal linear amplification step used an additional DNA/RNA chimeric primer, DNA polymerase and RNase H in an isothermal reaction creating antisense strand cDNA The cDNA was fragmented to produce a uniform distribution of short cDNAs and biotin labeled using the NuGEN Ovation FLv2 reagents. 3.4µg each of labeled target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.
| | Sample_hyb_protocol | The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 18 hours at 45 degrees C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 450s (Affymetrix, Santa Clara, CA) using the FS450_0004 Affymetrix fluidics script. Hybridization date: 01/28/08; Array lot: 4035270
| | Sample_scan_protocol | The distribution of fluorescent material on the processed array was determined using the Affymetrix GS300 Scanner with the 7G upgrade. The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.
| | Sample_data_processing | The data were processed by GeneSifter software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Grover,C,Bagby, MD
| | Sample_contact_email | grover@ohsu.edu
| | Sample_contact_laboratory | Knight Cancer Institute
| | Sample_contact_department | Dept. of Medicine
| | Sample_contact_institute | Oregon Health & Science University
| | Sample_contact_address | 3181 SW Sam Jackson Park Rd.
| | Sample_contact_city | Portland
| | Sample_contact_state | OR
| | Sample_contact_zip/postal_code | 97239
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM751nnn/GSM751547/suppl/GSM751547.CEL.gz
| | Sample_series_id | GSE30318
| | Sample_data_row_count | 45101
| | |
|
GSM751548 | GPL1261 |
|
mutant_no TNF_rep3
|
c-Kit+Sca-1+Lin- bone marrow cells from Fancc mutant mouse, cultured in growth factors alone
|
genotype/variation: Fancc-/-
age: 2-4 months
cell type: hematopoietic progenitor cells
|
|
| Sample_geo_accession | GSM751548
| | Sample_status | Public on May 23 2012
| | Sample_submission_date | Jun 30 2011
| | Sample_last_update_date | May 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Immediately after plating cells, half of the samples were treated with 10 ng/ml TNF alpha for 24 hours before RNA harvest. The other half of the samples received medium alone.
| | Sample_growth_protocol_ch1 | Freshly-isolated KSL cells were placed into culture dishes at a density of 104 per ml medium. Medium was RPMI containing 10% fetal bovine serum, 20 ng/ml IL-6, 10 ng/ml IL-11, 50 ng/ml Flt3L, and 10 ng/ml SCF.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected from medium by centrifugation, lysed with 75 ul QIAGEN RLT buffer, then RNA extracted with the QIAGEN Rneasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to amplified cDNA using the NuGEN Ovation RNA amplification v.2 System. Using between 5-15ng of total RNA as input, in a three step process, total RNA was converted to cDNA: (1) First Strand Synthesis: Single stranded cDNA was prepared from total RNA using a chimeric DNA/RNA primers and reverse transcriptase, (Step 2) Second Strand Synthesis: After partial fragmentation of mRNA in the cDNA/mRNA complex, DNA polymerase generated a second strand, (3) SPIA Amplification: The isothermal linear amplification step used an additional DNA/RNA chimeric primer, DNA polymerase and RNase H in an isothermal reaction creating antisense strand cDNA The cDNA was fragmented to produce a uniform distribution of short cDNAs and biotin labeled using the NuGEN Ovation FLv2 reagents. 3.4µg each of labeled target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.
| | Sample_hyb_protocol | The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 18 hours at 45 degrees C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 450s (Affymetrix, Santa Clara, CA) using the FS450_0004 Affymetrix fluidics script. Hybridization date: 01/28/08; Array lot: 4035270
| | Sample_scan_protocol | The distribution of fluorescent material on the processed array was determined using the Affymetrix GS300 Scanner with the 7G upgrade. The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.
| | Sample_data_processing | The data were processed by GeneSifter software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Grover,C,Bagby, MD
| | Sample_contact_email | grover@ohsu.edu
| | Sample_contact_laboratory | Knight Cancer Institute
| | Sample_contact_department | Dept. of Medicine
| | Sample_contact_institute | Oregon Health & Science University
| | Sample_contact_address | 3181 SW Sam Jackson Park Rd.
| | Sample_contact_city | Portland
| | Sample_contact_state | OR
| | Sample_contact_zip/postal_code | 97239
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM751nnn/GSM751548/suppl/GSM751548.CEL.gz
| | Sample_series_id | GSE30318
| | Sample_data_row_count | 45101
| | |
|
GSM751549 | GPL1261 |
|
wild-type_with TNF_rep1
|
c-Kit+Sca-1+Lin- bone marrow cells from wild-type mouse, cultured in growth factors plus TNF
|
genotype/variation: wild-type
age: 2-4 months
cell type: hematopoietic progenitor cells
|
|
| Sample_geo_accession | GSM751549
| | Sample_status | Public on May 23 2012
| | Sample_submission_date | Jun 30 2011
| | Sample_last_update_date | May 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Immediately after plating cells, half of the samples were treated with 10 ng/ml TNF alpha for 24 hours before RNA harvest. The other half of the samples received medium alone.
| | Sample_growth_protocol_ch1 | Freshly-isolated KSL cells were placed into culture dishes at a density of 104 per ml medium. Medium was RPMI containing 10% fetal bovine serum, 20 ng/ml IL-6, 10 ng/ml IL-11, 50 ng/ml Flt3L, and 10 ng/ml SCF.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected from medium by centrifugation, lysed with 75 ul QIAGEN RLT buffer, then RNA extracted with the QIAGEN Rneasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to amplified cDNA using the NuGEN Ovation RNA amplification v.2 System. Using between 5-15ng of total RNA as input, in a three step process, total RNA was converted to cDNA: (1) First Strand Synthesis: Single stranded cDNA was prepared from total RNA using a chimeric DNA/RNA primers and reverse transcriptase, (Step 2) Second Strand Synthesis: After partial fragmentation of mRNA in the cDNA/mRNA complex, DNA polymerase generated a second strand, (3) SPIA Amplification: The isothermal linear amplification step used an additional DNA/RNA chimeric primer, DNA polymerase and RNase H in an isothermal reaction creating antisense strand cDNA The cDNA was fragmented to produce a uniform distribution of short cDNAs and biotin labeled using the NuGEN Ovation FLv2 reagents. 3.4µg each of labeled target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.
| | Sample_hyb_protocol | The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 18 hours at 45 degrees C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 450s (Affymetrix, Santa Clara, CA) using the FS450_0004 Affymetrix fluidics script. Hybridization date: 01/28/08; Array lot: 4035270
| | Sample_scan_protocol | The distribution of fluorescent material on the processed array was determined using the Affymetrix GS300 Scanner with the 7G upgrade. The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.
| | Sample_data_processing | The data were processed by GeneSifter software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Grover,C,Bagby, MD
| | Sample_contact_email | grover@ohsu.edu
| | Sample_contact_laboratory | Knight Cancer Institute
| | Sample_contact_department | Dept. of Medicine
| | Sample_contact_institute | Oregon Health & Science University
| | Sample_contact_address | 3181 SW Sam Jackson Park Rd.
| | Sample_contact_city | Portland
| | Sample_contact_state | OR
| | Sample_contact_zip/postal_code | 97239
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM751nnn/GSM751549/suppl/GSM751549.CEL.gz
| | Sample_series_id | GSE30318
| | Sample_data_row_count | 45101
| | |
|
GSM751550 | GPL1261 |
|
wild-type_with TNF_rep2
|
c-Kit+Sca-1+Lin- bone marrow cells from wild-type mouse, cultured in growth factors plus TNF
|
genotype/variation: wild-type
age: 2-4 months
cell type: hematopoietic progenitor cells
|
|
| Sample_geo_accession | GSM751550
| | Sample_status | Public on May 23 2012
| | Sample_submission_date | Jun 30 2011
| | Sample_last_update_date | May 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Immediately after plating cells, half of the samples were treated with 10 ng/ml TNF alpha for 24 hours before RNA harvest. The other half of the samples received medium alone.
| | Sample_growth_protocol_ch1 | Freshly-isolated KSL cells were placed into culture dishes at a density of 104 per ml medium. Medium was RPMI containing 10% fetal bovine serum, 20 ng/ml IL-6, 10 ng/ml IL-11, 50 ng/ml Flt3L, and 10 ng/ml SCF.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected from medium by centrifugation, lysed with 75 ul QIAGEN RLT buffer, then RNA extracted with the QIAGEN Rneasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to amplified cDNA using the NuGEN Ovation RNA amplification v.2 System. Using between 5-15ng of total RNA as input, in a three step process, total RNA was converted to cDNA: (1) First Strand Synthesis: Single stranded cDNA was prepared from total RNA using a chimeric DNA/RNA primers and reverse transcriptase, (Step 2) Second Strand Synthesis: After partial fragmentation of mRNA in the cDNA/mRNA complex, DNA polymerase generated a second strand, (3) SPIA Amplification: The isothermal linear amplification step used an additional DNA/RNA chimeric primer, DNA polymerase and RNase H in an isothermal reaction creating antisense strand cDNA The cDNA was fragmented to produce a uniform distribution of short cDNAs and biotin labeled using the NuGEN Ovation FLv2 reagents. 3.4µg each of labeled target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.
| | Sample_hyb_protocol | The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 18 hours at 45 degrees C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 450s (Affymetrix, Santa Clara, CA) using the FS450_0004 Affymetrix fluidics script. Hybridization date: 01/28/08; Array lot: 4035270
| | Sample_scan_protocol | The distribution of fluorescent material on the processed array was determined using the Affymetrix GS300 Scanner with the 7G upgrade. The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.
| | Sample_data_processing | The data were processed by GeneSifter software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Grover,C,Bagby, MD
| | Sample_contact_email | grover@ohsu.edu
| | Sample_contact_laboratory | Knight Cancer Institute
| | Sample_contact_department | Dept. of Medicine
| | Sample_contact_institute | Oregon Health & Science University
| | Sample_contact_address | 3181 SW Sam Jackson Park Rd.
| | Sample_contact_city | Portland
| | Sample_contact_state | OR
| | Sample_contact_zip/postal_code | 97239
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM751nnn/GSM751550/suppl/GSM751550.CEL.gz
| | Sample_series_id | GSE30318
| | Sample_data_row_count | 45101
| | |
|
GSM751551 | GPL1261 |
|
wild-type_with TNF_rep3
|
c-Kit+Sca-1+Lin- bone marrow cells from wild-type mouse, cultured in growth factors plus TNF
|
genotype/variation: wild-type
age: 2-4 months
cell type: hematopoietic progenitor cells
|
|
| Sample_geo_accession | GSM751551
| | Sample_status | Public on May 23 2012
| | Sample_submission_date | Jun 30 2011
| | Sample_last_update_date | May 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Immediately after plating cells, half of the samples were treated with 10 ng/ml TNF alpha for 24 hours before RNA harvest. The other half of the samples received medium alone.
| | Sample_growth_protocol_ch1 | Freshly-isolated KSL cells were placed into culture dishes at a density of 104 per ml medium. Medium was RPMI containing 10% fetal bovine serum, 20 ng/ml IL-6, 10 ng/ml IL-11, 50 ng/ml Flt3L, and 10 ng/ml SCF.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected from medium by centrifugation, lysed with 75 ul QIAGEN RLT buffer, then RNA extracted with the QIAGEN Rneasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to amplified cDNA using the NuGEN Ovation RNA amplification v.2 System. Using between 5-15ng of total RNA as input, in a three step process, total RNA was converted to cDNA: (1) First Strand Synthesis: Single stranded cDNA was prepared from total RNA using a chimeric DNA/RNA primers and reverse transcriptase, (Step 2) Second Strand Synthesis: After partial fragmentation of mRNA in the cDNA/mRNA complex, DNA polymerase generated a second strand, (3) SPIA Amplification: The isothermal linear amplification step used an additional DNA/RNA chimeric primer, DNA polymerase and RNase H in an isothermal reaction creating antisense strand cDNA The cDNA was fragmented to produce a uniform distribution of short cDNAs and biotin labeled using the NuGEN Ovation FLv2 reagents. 3.4µg each of labeled target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.
| | Sample_hyb_protocol | The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 18 hours at 45 degrees C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 450s (Affymetrix, Santa Clara, CA) using the FS450_0004 Affymetrix fluidics script. Hybridization date: 01/28/08; Array lot: 4035270
| | Sample_scan_protocol | The distribution of fluorescent material on the processed array was determined using the Affymetrix GS300 Scanner with the 7G upgrade. The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.
| | Sample_data_processing | The data were processed by GeneSifter software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Grover,C,Bagby, MD
| | Sample_contact_email | grover@ohsu.edu
| | Sample_contact_laboratory | Knight Cancer Institute
| | Sample_contact_department | Dept. of Medicine
| | Sample_contact_institute | Oregon Health & Science University
| | Sample_contact_address | 3181 SW Sam Jackson Park Rd.
| | Sample_contact_city | Portland
| | Sample_contact_state | OR
| | Sample_contact_zip/postal_code | 97239
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM751nnn/GSM751551/suppl/GSM751551.CEL.gz
| | Sample_series_id | GSE30318
| | Sample_data_row_count | 45101
| | |
|
GSM751552 | GPL1261 |
|
mutant_with TNF_rep1
|
c-Kit+Sca-1+Lin- bone marrow cells from Fancc mutant mouse, cultured in growth factors plus TNF
|
genotype/variation: Fancc-/-
age: 2-4 months
cell type: hematopoietic progenitor cells
|
|
| Sample_geo_accession | GSM751552
| | Sample_status | Public on May 23 2012
| | Sample_submission_date | Jun 30 2011
| | Sample_last_update_date | May 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Immediately after plating cells, half of the samples were treated with 10 ng/ml TNF alpha for 24 hours before RNA harvest. The other half of the samples received medium alone.
| | Sample_growth_protocol_ch1 | Freshly-isolated KSL cells were placed into culture dishes at a density of 104 per ml medium. Medium was RPMI containing 10% fetal bovine serum, 20 ng/ml IL-6, 10 ng/ml IL-11, 50 ng/ml Flt3L, and 10 ng/ml SCF.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected from medium by centrifugation, lysed with 75 ul QIAGEN RLT buffer, then RNA extracted with the QIAGEN Rneasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to amplified cDNA using the NuGEN Ovation RNA amplification v.2 System. Using between 5-15ng of total RNA as input, in a three step process, total RNA was converted to cDNA: (1) First Strand Synthesis: Single stranded cDNA was prepared from total RNA using a chimeric DNA/RNA primers and reverse transcriptase, (Step 2) Second Strand Synthesis: After partial fragmentation of mRNA in the cDNA/mRNA complex, DNA polymerase generated a second strand, (3) SPIA Amplification: The isothermal linear amplification step used an additional DNA/RNA chimeric primer, DNA polymerase and RNase H in an isothermal reaction creating antisense strand cDNA The cDNA was fragmented to produce a uniform distribution of short cDNAs and biotin labeled using the NuGEN Ovation FLv2 reagents. 3.4µg each of labeled target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.
| | Sample_hyb_protocol | The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 18 hours at 45 degrees C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 450s (Affymetrix, Santa Clara, CA) using the FS450_0004 Affymetrix fluidics script. Hybridization date: 01/28/08; Array lot: 4035270
| | Sample_scan_protocol | The distribution of fluorescent material on the processed array was determined using the Affymetrix GS300 Scanner with the 7G upgrade. The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.
| | Sample_data_processing | The data were processed by GeneSifter software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Grover,C,Bagby, MD
| | Sample_contact_email | grover@ohsu.edu
| | Sample_contact_laboratory | Knight Cancer Institute
| | Sample_contact_department | Dept. of Medicine
| | Sample_contact_institute | Oregon Health & Science University
| | Sample_contact_address | 3181 SW Sam Jackson Park Rd.
| | Sample_contact_city | Portland
| | Sample_contact_state | OR
| | Sample_contact_zip/postal_code | 97239
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM751nnn/GSM751552/suppl/GSM751552.CEL.gz
| | Sample_series_id | GSE30318
| | Sample_data_row_count | 45101
| | |
|
GSM751553 | GPL1261 |
|
mutant_with TNF_rep2
|
c-Kit+Sca-1+Lin- bone marrow cells from Fancc mutant mouse, cultured in growth factors plus TNF
|
genotype/variation: Fancc-/-
age: 2-4 months
cell type: hematopoietic progenitor cells
|
|
| Sample_geo_accession | GSM751553
| | Sample_status | Public on May 23 2012
| | Sample_submission_date | Jun 30 2011
| | Sample_last_update_date | May 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Immediately after plating cells, half of the samples were treated with 10 ng/ml TNF alpha for 24 hours before RNA harvest. The other half of the samples received medium alone.
| | Sample_growth_protocol_ch1 | Freshly-isolated KSL cells were placed into culture dishes at a density of 104 per ml medium. Medium was RPMI containing 10% fetal bovine serum, 20 ng/ml IL-6, 10 ng/ml IL-11, 50 ng/ml Flt3L, and 10 ng/ml SCF.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected from medium by centrifugation, lysed with 75 ul QIAGEN RLT buffer, then RNA extracted with the QIAGEN Rneasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to amplified cDNA using the NuGEN Ovation RNA amplification v.2 System. Using between 5-15ng of total RNA as input, in a three step process, total RNA was converted to cDNA: (1) First Strand Synthesis: Single stranded cDNA was prepared from total RNA using a chimeric DNA/RNA primers and reverse transcriptase, (Step 2) Second Strand Synthesis: After partial fragmentation of mRNA in the cDNA/mRNA complex, DNA polymerase generated a second strand, (3) SPIA Amplification: The isothermal linear amplification step used an additional DNA/RNA chimeric primer, DNA polymerase and RNase H in an isothermal reaction creating antisense strand cDNA The cDNA was fragmented to produce a uniform distribution of short cDNAs and biotin labeled using the NuGEN Ovation FLv2 reagents. 3.4µg each of labeled target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.
| | Sample_hyb_protocol | The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 18 hours at 45 degrees C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 450s (Affymetrix, Santa Clara, CA) using the FS450_0004 Affymetrix fluidics script. Hybridization date: 01/28/08; Array lot: 4035270
| | Sample_scan_protocol | The distribution of fluorescent material on the processed array was determined using the Affymetrix GS300 Scanner with the 7G upgrade. The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.
| | Sample_data_processing | The data were processed by GeneSifter software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Grover,C,Bagby, MD
| | Sample_contact_email | grover@ohsu.edu
| | Sample_contact_laboratory | Knight Cancer Institute
| | Sample_contact_department | Dept. of Medicine
| | Sample_contact_institute | Oregon Health & Science University
| | Sample_contact_address | 3181 SW Sam Jackson Park Rd.
| | Sample_contact_city | Portland
| | Sample_contact_state | OR
| | Sample_contact_zip/postal_code | 97239
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM751nnn/GSM751553/suppl/GSM751553.CEL.gz
| | Sample_series_id | GSE30318
| | Sample_data_row_count | 45101
| | |
|
GSM751554 | GPL1261 |
|
mutant_with TNF_rep3
|
c-Kit+Sca-1+Lin- bone marrow cells from Fancc mutant mouse, cultured in growth factors plus TNF
|
genotype/variation: Fancc-/-
age: 2-4 months
cell type: hematopoietic progenitor cells
|
|
| Sample_geo_accession | GSM751554
| | Sample_status | Public on May 23 2012
| | Sample_submission_date | Jun 30 2011
| | Sample_last_update_date | May 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Immediately after plating cells, half of the samples were treated with 10 ng/ml TNF alpha for 24 hours before RNA harvest. The other half of the samples received medium alone.
| | Sample_growth_protocol_ch1 | Freshly-isolated KSL cells were placed into culture dishes at a density of 104 per ml medium. Medium was RPMI containing 10% fetal bovine serum, 20 ng/ml IL-6, 10 ng/ml IL-11, 50 ng/ml Flt3L, and 10 ng/ml SCF.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were collected from medium by centrifugation, lysed with 75 ul QIAGEN RLT buffer, then RNA extracted with the QIAGEN Rneasy Micro Kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to amplified cDNA using the NuGEN Ovation RNA amplification v.2 System. Using between 5-15ng of total RNA as input, in a three step process, total RNA was converted to cDNA: (1) First Strand Synthesis: Single stranded cDNA was prepared from total RNA using a chimeric DNA/RNA primers and reverse transcriptase, (Step 2) Second Strand Synthesis: After partial fragmentation of mRNA in the cDNA/mRNA complex, DNA polymerase generated a second strand, (3) SPIA Amplification: The isothermal linear amplification step used an additional DNA/RNA chimeric primer, DNA polymerase and RNase H in an isothermal reaction creating antisense strand cDNA The cDNA was fragmented to produce a uniform distribution of short cDNAs and biotin labeled using the NuGEN Ovation FLv2 reagents. 3.4µg each of labeled target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.
| | Sample_hyb_protocol | The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 18 hours at 45 degrees C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 450s (Affymetrix, Santa Clara, CA) using the FS450_0004 Affymetrix fluidics script. Hybridization date: 01/28/08; Array lot: 4035270
| | Sample_scan_protocol | The distribution of fluorescent material on the processed array was determined using the Affymetrix GS300 Scanner with the 7G upgrade. The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.
| | Sample_data_processing | The data were processed by GeneSifter software using Robust Multichip Analysis (RMA) that includes a background correction, quantile normalization, and median polish as summarization.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Grover,C,Bagby, MD
| | Sample_contact_email | grover@ohsu.edu
| | Sample_contact_laboratory | Knight Cancer Institute
| | Sample_contact_department | Dept. of Medicine
| | Sample_contact_institute | Oregon Health & Science University
| | Sample_contact_address | 3181 SW Sam Jackson Park Rd.
| | Sample_contact_city | Portland
| | Sample_contact_state | OR
| | Sample_contact_zip/postal_code | 97239
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM751nnn/GSM751554/suppl/GSM751554.CEL.gz
| | Sample_series_id | GSE30318
| | Sample_data_row_count | 45101
| | |
|
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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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