Search results for the GEO ID: GSE29348  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM725465 | GPL1261 |
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WT HSCs, Biological rep1
|
WT HSCs
|
strain: C57BL/6 (B6)
cell type: HSCs
genotype/variation: WT
age: 8 weeks
|
Gene expression data from WT HSCs
|
| Sample_geo_accession | GSM725465
| | Sample_status | Public on May 17 2011
| | Sample_submission_date | May 17 2011
| | Sample_last_update_date | May 17 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | We compare the gene profile of HSCs between WT and Alox15-/- mice. Bone marrow cells were isolated and subsequently sorted by FACS for HSCs (Lin-c-Kit+Sca-1+) .
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA is isolated by following the protocol for the RNeasy Micro Kit, and quality is assessed using a 2100 Bioanalyzer instrument and RNA 6000 Pico LabChip assay (Agilent Technologies, Palo Alto, CA). Utilizing the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix, Santa Clara, CA.) between 100-300ng of total RNA undergoes reverse transcription with random hexamers tagged with T7 sequence. The double stranded cDNA that is generated is then amplified by T7 RNA polymerase to produce cRNA. Second cycle first strand cDNA synthesis then takes place incorporating dUTP which is later used as sites where fragmentation occurs by utilizing an uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 enzyme mix.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The fragmented cDNA is then labeled by terminal transferase attaching a biotin molecule using Affymetrix proprietary DNA labeling Reagent.
| | Sample_hyb_protocol | Approximately 2.0µg of fragmented and biotin-labeled cDNA is then hybridized onto a Mouse Gene ST 1.0 Array (Affymetrix, Santa Clara, CA.) for 16 hours at 45°C. Post-hybridization staining and washing are performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).
| | Sample_scan_protocol | the arrays are scanned with a GeneChip Scanner 3000. Images are acquired and cel files generated which are then used for analysis.
| | Sample_data_processing | DNA microarray analysis was carried out to compare gene expression between WT HSCs and Alox15-/- HSCs.
| | Sample_data_processing | Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method which incorporates convolution background correction and a summarization based on a multi-array model fit robustly using the median polish algorithm. These values were read into R/maanova and quantile-normalized. For this experiment, three pairwise comparisons will be used to statistically resolve gene expression differences between strain groups using the R/maanova analysis package (Wu et al. 2003). Specifically, differentially expressed genes will be detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova package (Cui et al. 2005, Wu et.al 2003). Statistical significance levels of the pairwise comparison will be calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method (Storey, 2002). Differentially expressed genes are declared at an FDR q-value threshold of 0.05.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | shaoguang,,Li
| | Sample_contact_email | shaoguang.li@umassmed.edu
| | Sample_contact_phone | 5088561691
| | Sample_contact_institute | Worcester
| | Sample_contact_address | 364 Plantation street
| | Sample_contact_city | Worcester
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01609
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM725nnn/GSM725465/suppl/GSM725465_GC_430_2_GES08_0108_050808_1.CEL.gz
| | Sample_series_id | GSE29348
| | Sample_data_row_count | 45101
| | |
|
GSM725466 | GPL1261 |
|
WT HSCs, Biological rep2
|
WT HSCs
|
strain: C57BL/6 (B6)
cell type: HSCs
genotype/variation: WT
age: 8 weeks
|
Gene expression data from WT HSCs
|
| Sample_geo_accession | GSM725466
| | Sample_status | Public on May 17 2011
| | Sample_submission_date | May 17 2011
| | Sample_last_update_date | May 17 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | We compare the gene profile of HSCs between WT and Alox15-/- mice. Bone marrow cells were isolated and subsequently sorted by FACS for HSCs (Lin-c-Kit+Sca-1+) .
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA is isolated by following the protocol for the RNeasy Micro Kit, and quality is assessed using a 2100 Bioanalyzer instrument and RNA 6000 Pico LabChip assay (Agilent Technologies, Palo Alto, CA). Utilizing the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix, Santa Clara, CA.) between 100-300ng of total RNA undergoes reverse transcription with random hexamers tagged with T7 sequence. The double stranded cDNA that is generated is then amplified by T7 RNA polymerase to produce cRNA. Second cycle first strand cDNA synthesis then takes place incorporating dUTP which is later used as sites where fragmentation occurs by utilizing an uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 enzyme mix.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The fragmented cDNA is then labeled by terminal transferase attaching a biotin molecule using Affymetrix proprietary DNA labeling Reagent.
| | Sample_hyb_protocol | Approximately 2.0µg of fragmented and biotin-labeled cDNA is then hybridized onto a Mouse Gene ST 1.0 Array (Affymetrix, Santa Clara, CA.) for 16 hours at 45°C. Post-hybridization staining and washing are performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).
| | Sample_scan_protocol | the arrays are scanned with a GeneChip Scanner 3000. Images are acquired and cel files generated which are then used for analysis.
| | Sample_data_processing | DNA microarray analysis was carried out to compare gene expression between WT HSCs and Alox15-/- HSCs.
| | Sample_data_processing | Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method which incorporates convolution background correction and a summarization based on a multi-array model fit robustly using the median polish algorithm. These values were read into R/maanova and quantile-normalized. For this experiment, three pairwise comparisons will be used to statistically resolve gene expression differences between strain groups using the R/maanova analysis package (Wu et al. 2003). Specifically, differentially expressed genes will be detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova package (Cui et al. 2005, Wu et.al 2003). Statistical significance levels of the pairwise comparison will be calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method (Storey, 2002). Differentially expressed genes are declared at an FDR q-value threshold of 0.05.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | shaoguang,,Li
| | Sample_contact_email | shaoguang.li@umassmed.edu
| | Sample_contact_phone | 5088561691
| | Sample_contact_institute | Worcester
| | Sample_contact_address | 364 Plantation street
| | Sample_contact_city | Worcester
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01609
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM725nnn/GSM725466/suppl/GSM725466_GC_430_2_GES08_0109_050808_1.CEL.gz
| | Sample_series_id | GSE29348
| | Sample_data_row_count | 45101
| | |
|
GSM725467 | GPL1261 |
|
Alox15-/- HSCs, Biological rep1
|
Alox15-/- HSCs
|
strain: C57BL/6 (B6)
cell type: HSCs
genotype/variation: Alox15-/-
age: 8 weeks
|
Gene expression data from Alox15-/- HSCs
|
| Sample_geo_accession | GSM725467
| | Sample_status | Public on May 17 2011
| | Sample_submission_date | May 17 2011
| | Sample_last_update_date | May 17 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | We compare the gene profile of HSCs between WT and Alox15-/- mice. Bone marrow cells were isolated and subsequently sorted by FACS for HSCs (Lin-c-Kit+Sca-1+) .
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA is isolated by following the protocol for the RNeasy Micro Kit, and quality is assessed using a 2100 Bioanalyzer instrument and RNA 6000 Pico LabChip assay (Agilent Technologies, Palo Alto, CA). Utilizing the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix, Santa Clara, CA.) between 100-300ng of total RNA undergoes reverse transcription with random hexamers tagged with T7 sequence. The double stranded cDNA that is generated is then amplified by T7 RNA polymerase to produce cRNA. Second cycle first strand cDNA synthesis then takes place incorporating dUTP which is later used as sites where fragmentation occurs by utilizing an uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 enzyme mix.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The fragmented cDNA is then labeled by terminal transferase attaching a biotin molecule using Affymetrix proprietary DNA labeling Reagent.
| | Sample_hyb_protocol | Approximately 2.0µg of fragmented and biotin-labeled cDNA is then hybridized onto a Mouse Gene ST 1.0 Array (Affymetrix, Santa Clara, CA.) for 16 hours at 45°C. Post-hybridization staining and washing are performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).
| | Sample_scan_protocol | the arrays are scanned with a GeneChip Scanner 3000. Images are acquired and cel files generated which are then used for analysis.
| | Sample_data_processing | DNA microarray analysis was carried out to compare gene expression between WT HSCs and Alox15-/- HSCs.
| | Sample_data_processing | Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method which incorporates convolution background correction and a summarization based on a multi-array model fit robustly using the median polish algorithm. These values were read into R/maanova and quantile-normalized. For this experiment, three pairwise comparisons will be used to statistically resolve gene expression differences between strain groups using the R/maanova analysis package (Wu et al. 2003). Specifically, differentially expressed genes will be detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova package (Cui et al. 2005, Wu et.al 2003). Statistical significance levels of the pairwise comparison will be calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method (Storey, 2002). Differentially expressed genes are declared at an FDR q-value threshold of 0.05.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | shaoguang,,Li
| | Sample_contact_email | shaoguang.li@umassmed.edu
| | Sample_contact_phone | 5088561691
| | Sample_contact_institute | Worcester
| | Sample_contact_address | 364 Plantation street
| | Sample_contact_city | Worcester
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01609
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM725nnn/GSM725467/suppl/GSM725467_GC_430_2_GES08_0110_050808_1.CEL.gz
| | Sample_series_id | GSE29348
| | Sample_data_row_count | 45101
| | |
|
GSM725468 | GPL1261 |
|
Alox15-/- HSCs, Biological rep2
|
Alox15-/- HSCs
|
strain: C57BL/6 (B6)
cell type: HSCs
genotype/variation: Alox15-/-
age: 8 weeks
|
Gene expression data from Alox15-/- HSCs
|
| Sample_geo_accession | GSM725468
| | Sample_status | Public on May 17 2011
| | Sample_submission_date | May 17 2011
| | Sample_last_update_date | May 17 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | We compare the gene profile of HSCs between WT and Alox15-/- mice. Bone marrow cells were isolated and subsequently sorted by FACS for HSCs (Lin-c-Kit+Sca-1+) .
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA is isolated by following the protocol for the RNeasy Micro Kit, and quality is assessed using a 2100 Bioanalyzer instrument and RNA 6000 Pico LabChip assay (Agilent Technologies, Palo Alto, CA). Utilizing the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix, Santa Clara, CA.) between 100-300ng of total RNA undergoes reverse transcription with random hexamers tagged with T7 sequence. The double stranded cDNA that is generated is then amplified by T7 RNA polymerase to produce cRNA. Second cycle first strand cDNA synthesis then takes place incorporating dUTP which is later used as sites where fragmentation occurs by utilizing an uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 enzyme mix.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The fragmented cDNA is then labeled by terminal transferase attaching a biotin molecule using Affymetrix proprietary DNA labeling Reagent.
| | Sample_hyb_protocol | Approximately 2.0µg of fragmented and biotin-labeled cDNA is then hybridized onto a Mouse Gene ST 1.0 Array (Affymetrix, Santa Clara, CA.) for 16 hours at 45°C. Post-hybridization staining and washing are performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).
| | Sample_scan_protocol | the arrays are scanned with a GeneChip Scanner 3000. Images are acquired and cel files generated which are then used for analysis.
| | Sample_data_processing | DNA microarray analysis was carried out to compare gene expression between WT HSCs and Alox15-/- HSCs.
| | Sample_data_processing | Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method which incorporates convolution background correction and a summarization based on a multi-array model fit robustly using the median polish algorithm. These values were read into R/maanova and quantile-normalized. For this experiment, three pairwise comparisons will be used to statistically resolve gene expression differences between strain groups using the R/maanova analysis package (Wu et al. 2003). Specifically, differentially expressed genes will be detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova package (Cui et al. 2005, Wu et.al 2003). Statistical significance levels of the pairwise comparison will be calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method (Storey, 2002). Differentially expressed genes are declared at an FDR q-value threshold of 0.05.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | shaoguang,,Li
| | Sample_contact_email | shaoguang.li@umassmed.edu
| | Sample_contact_phone | 5088561691
| | Sample_contact_institute | Worcester
| | Sample_contact_address | 364 Plantation street
| | Sample_contact_city | Worcester
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 01609
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM725nnn/GSM725468/suppl/GSM725468_GC_430_2_GES08_0111_050808_1.CEL.gz
| | Sample_series_id | GSE29348
| | Sample_data_row_count | 45101
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