Search results for the GEO ID: GSE47172  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1146007 | GPL96 |
|
Healthy control replicate 1
|
Healthy control replicate 1
|
tissue: Host peripheral blood
hiv status: HIV-
disease outcome: Alive
disease state: healthy control without invasive pneumococcal disease
|
Gene expression data from a healthy control without invasive pneumococcal disease.
|
| Sample_geo_accession | GSM1146007
| | Sample_status | Public on May 23 2013
| | Sample_submission_date | May 22 2013
| | Sample_last_update_date | May 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Aliquots of 0.86 mL PAXgene™ reagent were put into 1 mL microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. The filled microtubes were stored at 80oC until analysis.
| | Sample_growth_protocol_ch1 | Whole blood was drawn at admission from consecutive children with a presumptive diagnosis of bacterial meningitis.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from whole blood using an optimised method for the PAXgene blood RNA kit (Qiagen, West Sussex, UK), according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (2mg) was reverse transcribed into double stranded cDNA using the Superscript double stranded cDNA synthesis kit (Invitrogen, Paisley, UK) according to the manufacturers’ guidelines. The double stranded cDNA was purified using a GeneChip TM sample clean-up module (Invitrogen, Paisley, UK). The purified cDNA was then biotin labelled with the ENZO BioArray high yield RNA transcript labelling kit (Affymetrix, High Wycombe, UK) and cleaned with a cRNA clean-up module (Invitrogen, Paisley, UK).
| | Sample_hyb_protocol | Aliquots of labelled cRNA (20mg) were fragmented at 94°C for 35 minutes and then hybridized to a Human Genome U133A GeneChipTM array for 16 hours rotating at 60rpm at 45°C in a GeneChipTM Hybridization Oven 640 (Affymetrix, High Wycombe, UK). Each chip was washed and stained on a GeneChipTM Fluidics Station 450 (Affymetrix, High Wycombe, UK).
| | Sample_scan_protocol | GeneChips were scanned using a GeneChipTM Scanner 450 (Affymetrix, High Wycombe, UK) employing standard recommended protocols (Affymetrix, High Wycombe, UK).
| | Sample_data_processing | The data were analyzed with analysed using R and Bioconductor packages. Data were first loaded using the affy package, followed by pre-processing (background correction, normalization and summarisation of probe level data) using the rma function.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Benard,,Kulohoma
| | Sample_contact_email | bkulohoma@iscb.org
| | Sample_contact_institute | University of Liverpool
| | Sample_contact_address | Department of Women's and Children's Health, Institute of Translational Medicine, Alder Hey Children's Hospital
| | Sample_contact_city | Liverpool
| | Sample_contact_zip/postal_code | L12 2AP
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1146nnn/GSM1146007/suppl/GSM1146007_C13.CEL.gz
| | Sample_series_id | GSE47172
| | Sample_data_row_count | 22283
| | |
|
GSM1146008 | GPL96 |
|
Healthy control replicate 2
|
Healthy control replicate 2
|
tissue: Host peripheral blood
hiv status: HIV-
disease outcome: Alive
disease state: healthy control without invasive pneumococcal disease
|
Gene expression data from a healthy control without invasive pneumococcal disease.
|
| Sample_geo_accession | GSM1146008
| | Sample_status | Public on May 23 2013
| | Sample_submission_date | May 22 2013
| | Sample_last_update_date | May 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Aliquots of 0.86 mL PAXgene™ reagent were put into 1 mL microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. The filled microtubes were stored at 80oC until analysis.
| | Sample_growth_protocol_ch1 | Whole blood was drawn at admission from consecutive children with a presumptive diagnosis of bacterial meningitis.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from whole blood using an optimised method for the PAXgene blood RNA kit (Qiagen, West Sussex, UK), according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (2mg) was reverse transcribed into double stranded cDNA using the Superscript double stranded cDNA synthesis kit (Invitrogen, Paisley, UK) according to the manufacturers’ guidelines. The double stranded cDNA was purified using a GeneChip TM sample clean-up module (Invitrogen, Paisley, UK). The purified cDNA was then biotin labelled with the ENZO BioArray high yield RNA transcript labelling kit (Affymetrix, High Wycombe, UK) and cleaned with a cRNA clean-up module (Invitrogen, Paisley, UK).
| | Sample_hyb_protocol | Aliquots of labelled cRNA (20mg) were fragmented at 94°C for 35 minutes and then hybridized to a Human Genome U133A GeneChipTM array for 16 hours rotating at 60rpm at 45°C in a GeneChipTM Hybridization Oven 640 (Affymetrix, High Wycombe, UK). Each chip was washed and stained on a GeneChipTM Fluidics Station 450 (Affymetrix, High Wycombe, UK).
| | Sample_scan_protocol | GeneChips were scanned using a GeneChipTM Scanner 450 (Affymetrix, High Wycombe, UK) employing standard recommended protocols (Affymetrix, High Wycombe, UK).
| | Sample_data_processing | The data were analyzed with analysed using R and Bioconductor packages. Data were first loaded using the affy package, followed by pre-processing (background correction, normalization and summarisation of probe level data) using the rma function.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Benard,,Kulohoma
| | Sample_contact_email | bkulohoma@iscb.org
| | Sample_contact_institute | University of Liverpool
| | Sample_contact_address | Department of Women's and Children's Health, Institute of Translational Medicine, Alder Hey Children's Hospital
| | Sample_contact_city | Liverpool
| | Sample_contact_zip/postal_code | L12 2AP
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1146nnn/GSM1146008/suppl/GSM1146008_C8.CEL.gz
| | Sample_series_id | GSE47172
| | Sample_data_row_count | 22283
| | |
|
GSM1146009 | GPL96 |
|
Healthy control replicate 3
|
Healthy control replicate 3
|
tissue: Host peripheral blood
hiv status: HIV-
disease outcome: Alive
disease state: healthy control without invasive pneumococcal disease
|
Gene expression data from a healthy control without invasive pneumococcal disease.
|
| Sample_geo_accession | GSM1146009
| | Sample_status | Public on May 23 2013
| | Sample_submission_date | May 22 2013
| | Sample_last_update_date | May 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Aliquots of 0.86 mL PAXgene™ reagent were put into 1 mL microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. The filled microtubes were stored at 80oC until analysis.
| | Sample_growth_protocol_ch1 | Whole blood was drawn at admission from consecutive children with a presumptive diagnosis of bacterial meningitis.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from whole blood using an optimised method for the PAXgene blood RNA kit (Qiagen, West Sussex, UK), according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (2mg) was reverse transcribed into double stranded cDNA using the Superscript double stranded cDNA synthesis kit (Invitrogen, Paisley, UK) according to the manufacturers’ guidelines. The double stranded cDNA was purified using a GeneChip TM sample clean-up module (Invitrogen, Paisley, UK). The purified cDNA was then biotin labelled with the ENZO BioArray high yield RNA transcript labelling kit (Affymetrix, High Wycombe, UK) and cleaned with a cRNA clean-up module (Invitrogen, Paisley, UK).
| | Sample_hyb_protocol | Aliquots of labelled cRNA (20mg) were fragmented at 94°C for 35 minutes and then hybridized to a Human Genome U133A GeneChipTM array for 16 hours rotating at 60rpm at 45°C in a GeneChipTM Hybridization Oven 640 (Affymetrix, High Wycombe, UK). Each chip was washed and stained on a GeneChipTM Fluidics Station 450 (Affymetrix, High Wycombe, UK).
| | Sample_scan_protocol | GeneChips were scanned using a GeneChipTM Scanner 450 (Affymetrix, High Wycombe, UK) employing standard recommended protocols (Affymetrix, High Wycombe, UK).
| | Sample_data_processing | The data were analyzed with analysed using R and Bioconductor packages. Data were first loaded using the affy package, followed by pre-processing (background correction, normalization and summarisation of probe level data) using the rma function.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Benard,,Kulohoma
| | Sample_contact_email | bkulohoma@iscb.org
| | Sample_contact_institute | University of Liverpool
| | Sample_contact_address | Department of Women's and Children's Health, Institute of Translational Medicine, Alder Hey Children's Hospital
| | Sample_contact_city | Liverpool
| | Sample_contact_zip/postal_code | L12 2AP
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1146nnn/GSM1146009/suppl/GSM1146009_C9.CEL.gz
| | Sample_series_id | GSE47172
| | Sample_data_row_count | 22283
| | |
|
GSM1146010 | GPL96 |
|
Deceased HIV+ case replicate 1
|
Deceased HIV+ case replicate 1
|
tissue: Host peripheral blood
hiv status: HIV+
disease outcome: Dead
disease state: HIV+ case with invasive pneumococcal disease
|
Gene expression data from a deceased HIV+ case with invasive pneumococcal disease.
|
| Sample_geo_accession | GSM1146010
| | Sample_status | Public on May 23 2013
| | Sample_submission_date | May 22 2013
| | Sample_last_update_date | May 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Aliquots of 0.86 mL PAXgene™ reagent were put into 1 mL microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. The filled microtubes were stored at 80oC until analysis.
| | Sample_growth_protocol_ch1 | Whole blood was drawn at admission from consecutive children with a presumptive diagnosis of bacterial meningitis.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from whole blood using an optimised method for the PAXgene blood RNA kit (Qiagen, West Sussex, UK), according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (2mg) was reverse transcribed into double stranded cDNA using the Superscript double stranded cDNA synthesis kit (Invitrogen, Paisley, UK) according to the manufacturers’ guidelines. The double stranded cDNA was purified using a GeneChip TM sample clean-up module (Invitrogen, Paisley, UK). The purified cDNA was then biotin labelled with the ENZO BioArray high yield RNA transcript labelling kit (Affymetrix, High Wycombe, UK) and cleaned with a cRNA clean-up module (Invitrogen, Paisley, UK).
| | Sample_hyb_protocol | Aliquots of labelled cRNA (20mg) were fragmented at 94°C for 35 minutes and then hybridized to a Human Genome U133A GeneChipTM array for 16 hours rotating at 60rpm at 45°C in a GeneChipTM Hybridization Oven 640 (Affymetrix, High Wycombe, UK). Each chip was washed and stained on a GeneChipTM Fluidics Station 450 (Affymetrix, High Wycombe, UK).
| | Sample_scan_protocol | GeneChips were scanned using a GeneChipTM Scanner 450 (Affymetrix, High Wycombe, UK) employing standard recommended protocols (Affymetrix, High Wycombe, UK).
| | Sample_data_processing | The data were analyzed with analysed using R and Bioconductor packages. Data were first loaded using the affy package, followed by pre-processing (background correction, normalization and summarisation of probe level data) using the rma function.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Benard,,Kulohoma
| | Sample_contact_email | bkulohoma@iscb.org
| | Sample_contact_institute | University of Liverpool
| | Sample_contact_address | Department of Women's and Children's Health, Institute of Translational Medicine, Alder Hey Children's Hospital
| | Sample_contact_city | Liverpool
| | Sample_contact_zip/postal_code | L12 2AP
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1146nnn/GSM1146010/suppl/GSM1146010_94.CEL.gz
| | Sample_series_id | GSE47172
| | Sample_data_row_count | 22283
| | |
|
GSM1146011 | GPL96 |
|
Deceased HIV+ case replicate 2
|
Deceased HIV+ case replicate 2
|
tissue: Host peripheral blood
hiv status: HIV+
disease outcome: Dead
disease state: HIV+ case with invasive pneumococcal disease
|
Gene expression data from a deceased HIV+ case with invasive pneumococcal disease.
|
| Sample_geo_accession | GSM1146011
| | Sample_status | Public on May 23 2013
| | Sample_submission_date | May 22 2013
| | Sample_last_update_date | May 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Aliquots of 0.86 mL PAXgene™ reagent were put into 1 mL microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. The filled microtubes were stored at 80oC until analysis.
| | Sample_growth_protocol_ch1 | Whole blood was drawn at admission from consecutive children with a presumptive diagnosis of bacterial meningitis.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from whole blood using an optimised method for the PAXgene blood RNA kit (Qiagen, West Sussex, UK), according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (2mg) was reverse transcribed into double stranded cDNA using the Superscript double stranded cDNA synthesis kit (Invitrogen, Paisley, UK) according to the manufacturers’ guidelines. The double stranded cDNA was purified using a GeneChip TM sample clean-up module (Invitrogen, Paisley, UK). The purified cDNA was then biotin labelled with the ENZO BioArray high yield RNA transcript labelling kit (Affymetrix, High Wycombe, UK) and cleaned with a cRNA clean-up module (Invitrogen, Paisley, UK).
| | Sample_hyb_protocol | Aliquots of labelled cRNA (20mg) were fragmented at 94°C for 35 minutes and then hybridized to a Human Genome U133A GeneChipTM array for 16 hours rotating at 60rpm at 45°C in a GeneChipTM Hybridization Oven 640 (Affymetrix, High Wycombe, UK). Each chip was washed and stained on a GeneChipTM Fluidics Station 450 (Affymetrix, High Wycombe, UK).
| | Sample_scan_protocol | GeneChips were scanned using a GeneChipTM Scanner 450 (Affymetrix, High Wycombe, UK) employing standard recommended protocols (Affymetrix, High Wycombe, UK).
| | Sample_data_processing | The data were analyzed with analysed using R and Bioconductor packages. Data were first loaded using the affy package, followed by pre-processing (background correction, normalization and summarisation of probe level data) using the rma function.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Benard,,Kulohoma
| | Sample_contact_email | bkulohoma@iscb.org
| | Sample_contact_institute | University of Liverpool
| | Sample_contact_address | Department of Women's and Children's Health, Institute of Translational Medicine, Alder Hey Children's Hospital
| | Sample_contact_city | Liverpool
| | Sample_contact_zip/postal_code | L12 2AP
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1146nnn/GSM1146011/suppl/GSM1146011_95.CEL.gz
| | Sample_series_id | GSE47172
| | Sample_data_row_count | 22283
| | |
|
GSM1146012 | GPL96 |
|
Deceased HIV+ case replicate 3
|
Deceased HIV+ case replicate 3
|
tissue: Host peripheral blood
hiv status: HIV+
disease outcome: Dead
disease state: HIV+ case with invasive pneumococcal disease
|
Gene expression data from a deceased HIV+ case with invasive pneumococcal disease.
|
| Sample_geo_accession | GSM1146012
| | Sample_status | Public on May 23 2013
| | Sample_submission_date | May 22 2013
| | Sample_last_update_date | May 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Aliquots of 0.86 mL PAXgene™ reagent were put into 1 mL microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. The filled microtubes were stored at 80oC until analysis.
| | Sample_growth_protocol_ch1 | Whole blood was drawn at admission from consecutive children with a presumptive diagnosis of bacterial meningitis.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from whole blood using an optimised method for the PAXgene blood RNA kit (Qiagen, West Sussex, UK), according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (2mg) was reverse transcribed into double stranded cDNA using the Superscript double stranded cDNA synthesis kit (Invitrogen, Paisley, UK) according to the manufacturers’ guidelines. The double stranded cDNA was purified using a GeneChip TM sample clean-up module (Invitrogen, Paisley, UK). The purified cDNA was then biotin labelled with the ENZO BioArray high yield RNA transcript labelling kit (Affymetrix, High Wycombe, UK) and cleaned with a cRNA clean-up module (Invitrogen, Paisley, UK).
| | Sample_hyb_protocol | Aliquots of labelled cRNA (20mg) were fragmented at 94°C for 35 minutes and then hybridized to a Human Genome U133A GeneChipTM array for 16 hours rotating at 60rpm at 45°C in a GeneChipTM Hybridization Oven 640 (Affymetrix, High Wycombe, UK). Each chip was washed and stained on a GeneChipTM Fluidics Station 450 (Affymetrix, High Wycombe, UK).
| | Sample_scan_protocol | GeneChips were scanned using a GeneChipTM Scanner 450 (Affymetrix, High Wycombe, UK) employing standard recommended protocols (Affymetrix, High Wycombe, UK).
| | Sample_data_processing | The data were analyzed with analysed using R and Bioconductor packages. Data were first loaded using the affy package, followed by pre-processing (background correction, normalization and summarisation of probe level data) using the rma function.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Benard,,Kulohoma
| | Sample_contact_email | bkulohoma@iscb.org
| | Sample_contact_institute | University of Liverpool
| | Sample_contact_address | Department of Women's and Children's Health, Institute of Translational Medicine, Alder Hey Children's Hospital
| | Sample_contact_city | Liverpool
| | Sample_contact_zip/postal_code | L12 2AP
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1146nnn/GSM1146012/suppl/GSM1146012_97.CEL.gz
| | Sample_series_id | GSE47172
| | Sample_data_row_count | 22283
| | |
|
GSM1146013 | GPL96 |
|
Deceased HIV- case replicate 1
|
Deceased HIV- case replicate 1
|
tissue: Host peripheral blood
hiv status: HIV-
disease outcome: Dead
disease state: HIV- case with invasive pneumococcal disease
|
Gene expression data from a deceased HIV- case with invasive pneumococcal disease.
|
| Sample_geo_accession | GSM1146013
| | Sample_status | Public on May 23 2013
| | Sample_submission_date | May 22 2013
| | Sample_last_update_date | May 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Aliquots of 0.86 mL PAXgene™ reagent were put into 1 mL microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. The filled microtubes were stored at 80oC until analysis.
| | Sample_growth_protocol_ch1 | Whole blood was drawn at admission from consecutive children with a presumptive diagnosis of bacterial meningitis.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from whole blood using an optimised method for the PAXgene blood RNA kit (Qiagen, West Sussex, UK), according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (2mg) was reverse transcribed into double stranded cDNA using the Superscript double stranded cDNA synthesis kit (Invitrogen, Paisley, UK) according to the manufacturers’ guidelines. The double stranded cDNA was purified using a GeneChip TM sample clean-up module (Invitrogen, Paisley, UK). The purified cDNA was then biotin labelled with the ENZO BioArray high yield RNA transcript labelling kit (Affymetrix, High Wycombe, UK) and cleaned with a cRNA clean-up module (Invitrogen, Paisley, UK).
| | Sample_hyb_protocol | Aliquots of labelled cRNA (20mg) were fragmented at 94°C for 35 minutes and then hybridized to a Human Genome U133A GeneChipTM array for 16 hours rotating at 60rpm at 45°C in a GeneChipTM Hybridization Oven 640 (Affymetrix, High Wycombe, UK). Each chip was washed and stained on a GeneChipTM Fluidics Station 450 (Affymetrix, High Wycombe, UK).
| | Sample_scan_protocol | GeneChips were scanned using a GeneChipTM Scanner 450 (Affymetrix, High Wycombe, UK) employing standard recommended protocols (Affymetrix, High Wycombe, UK).
| | Sample_data_processing | The data were analyzed with analysed using R and Bioconductor packages. Data were first loaded using the affy package, followed by pre-processing (background correction, normalization and summarisation of probe level data) using the rma function.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Benard,,Kulohoma
| | Sample_contact_email | bkulohoma@iscb.org
| | Sample_contact_institute | University of Liverpool
| | Sample_contact_address | Department of Women's and Children's Health, Institute of Translational Medicine, Alder Hey Children's Hospital
| | Sample_contact_city | Liverpool
| | Sample_contact_zip/postal_code | L12 2AP
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1146nnn/GSM1146013/suppl/GSM1146013_115.CEL.gz
| | Sample_series_id | GSE47172
| | Sample_data_row_count | 22283
| | |
|
GSM1146014 | GPL96 |
|
Deceased HIV- case replicate 2
|
Deceased HIV- case replicate 2
|
tissue: Host peripheral blood
hiv status: HIV-
disease outcome: Dead
disease state: HIV- case with invasive pneumococcal disease
|
Gene expression data from a deceased HIV- case with invasive pneumococcal disease.
|
| Sample_geo_accession | GSM1146014
| | Sample_status | Public on May 23 2013
| | Sample_submission_date | May 22 2013
| | Sample_last_update_date | May 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Aliquots of 0.86 mL PAXgene™ reagent were put into 1 mL microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. The filled microtubes were stored at 80oC until analysis.
| | Sample_growth_protocol_ch1 | Whole blood was drawn at admission from consecutive children with a presumptive diagnosis of bacterial meningitis.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from whole blood using an optimised method for the PAXgene blood RNA kit (Qiagen, West Sussex, UK), according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (2mg) was reverse transcribed into double stranded cDNA using the Superscript double stranded cDNA synthesis kit (Invitrogen, Paisley, UK) according to the manufacturers’ guidelines. The double stranded cDNA was purified using a GeneChip TM sample clean-up module (Invitrogen, Paisley, UK). The purified cDNA was then biotin labelled with the ENZO BioArray high yield RNA transcript labelling kit (Affymetrix, High Wycombe, UK) and cleaned with a cRNA clean-up module (Invitrogen, Paisley, UK).
| | Sample_hyb_protocol | Aliquots of labelled cRNA (20mg) were fragmented at 94°C for 35 minutes and then hybridized to a Human Genome U133A GeneChipTM array for 16 hours rotating at 60rpm at 45°C in a GeneChipTM Hybridization Oven 640 (Affymetrix, High Wycombe, UK). Each chip was washed and stained on a GeneChipTM Fluidics Station 450 (Affymetrix, High Wycombe, UK).
| | Sample_scan_protocol | GeneChips were scanned using a GeneChipTM Scanner 450 (Affymetrix, High Wycombe, UK) employing standard recommended protocols (Affymetrix, High Wycombe, UK).
| | Sample_data_processing | The data were analyzed with analysed using R and Bioconductor packages. Data were first loaded using the affy package, followed by pre-processing (background correction, normalization and summarisation of probe level data) using the rma function.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Benard,,Kulohoma
| | Sample_contact_email | bkulohoma@iscb.org
| | Sample_contact_institute | University of Liverpool
| | Sample_contact_address | Department of Women's and Children's Health, Institute of Translational Medicine, Alder Hey Children's Hospital
| | Sample_contact_city | Liverpool
| | Sample_contact_zip/postal_code | L12 2AP
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1146nnn/GSM1146014/suppl/GSM1146014_121.CEL.gz
| | Sample_series_id | GSE47172
| | Sample_data_row_count | 22283
| | |
|
GSM1146015 | GPL96 |
|
Deceased HIV- case replicate 3
|
Deceased HIV- case replicate 3
|
tissue: Host peripheral blood
hiv status: HIV-
disease outcome: Dead
disease state: HIV- case with invasive pneumococcal disease
|
Gene expression data from a deceased HIV- case with invasive pneumococcal disease.
|
| Sample_geo_accession | GSM1146015
| | Sample_status | Public on May 23 2013
| | Sample_submission_date | May 22 2013
| | Sample_last_update_date | May 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Aliquots of 0.86 mL PAXgene™ reagent were put into 1 mL microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. The filled microtubes were stored at 80oC until analysis.
| | Sample_growth_protocol_ch1 | Whole blood was drawn at admission from consecutive children with a presumptive diagnosis of bacterial meningitis.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from whole blood using an optimised method for the PAXgene blood RNA kit (Qiagen, West Sussex, UK), according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (2mg) was reverse transcribed into double stranded cDNA using the Superscript double stranded cDNA synthesis kit (Invitrogen, Paisley, UK) according to the manufacturers’ guidelines. The double stranded cDNA was purified using a GeneChip TM sample clean-up module (Invitrogen, Paisley, UK). The purified cDNA was then biotin labelled with the ENZO BioArray high yield RNA transcript labelling kit (Affymetrix, High Wycombe, UK) and cleaned with a cRNA clean-up module (Invitrogen, Paisley, UK).
| | Sample_hyb_protocol | Aliquots of labelled cRNA (20mg) were fragmented at 94°C for 35 minutes and then hybridized to a Human Genome U133A GeneChipTM array for 16 hours rotating at 60rpm at 45°C in a GeneChipTM Hybridization Oven 640 (Affymetrix, High Wycombe, UK). Each chip was washed and stained on a GeneChipTM Fluidics Station 450 (Affymetrix, High Wycombe, UK).
| | Sample_scan_protocol | GeneChips were scanned using a GeneChipTM Scanner 450 (Affymetrix, High Wycombe, UK) employing standard recommended protocols (Affymetrix, High Wycombe, UK).
| | Sample_data_processing | The data were analyzed with analysed using R and Bioconductor packages. Data were first loaded using the affy package, followed by pre-processing (background correction, normalization and summarisation of probe level data) using the rma function.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Benard,,Kulohoma
| | Sample_contact_email | bkulohoma@iscb.org
| | Sample_contact_institute | University of Liverpool
| | Sample_contact_address | Department of Women's and Children's Health, Institute of Translational Medicine, Alder Hey Children's Hospital
| | Sample_contact_city | Liverpool
| | Sample_contact_zip/postal_code | L12 2AP
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1146nnn/GSM1146015/suppl/GSM1146015_82.CEL.gz
| | Sample_series_id | GSE47172
| | Sample_data_row_count | 22283
| | |
|
GSM1146016 | GPL96 |
|
Surviving HIV+ case replicate 1
|
Surviving HIV+ case replicate 1
|
tissue: Host peripheral blood
hiv status: HIV+
disease outcome: Alive
disease state: HIV+ case with invasive pneumococcal disease
|
Gene expression data from a surviving HIV+ case with invasive pneumococcal disease.
|
| Sample_geo_accession | GSM1146016
| | Sample_status | Public on May 23 2013
| | Sample_submission_date | May 22 2013
| | Sample_last_update_date | May 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Aliquots of 0.86 mL PAXgene™ reagent were put into 1 mL microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. The filled microtubes were stored at 80oC until analysis.
| | Sample_growth_protocol_ch1 | Whole blood was drawn at admission from consecutive children with a presumptive diagnosis of bacterial meningitis.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from whole blood using an optimised method for the PAXgene blood RNA kit (Qiagen, West Sussex, UK), according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (2mg) was reverse transcribed into double stranded cDNA using the Superscript double stranded cDNA synthesis kit (Invitrogen, Paisley, UK) according to the manufacturers’ guidelines. The double stranded cDNA was purified using a GeneChip TM sample clean-up module (Invitrogen, Paisley, UK). The purified cDNA was then biotin labelled with the ENZO BioArray high yield RNA transcript labelling kit (Affymetrix, High Wycombe, UK) and cleaned with a cRNA clean-up module (Invitrogen, Paisley, UK).
| | Sample_hyb_protocol | Aliquots of labelled cRNA (20mg) were fragmented at 94°C for 35 minutes and then hybridized to a Human Genome U133A GeneChipTM array for 16 hours rotating at 60rpm at 45°C in a GeneChipTM Hybridization Oven 640 (Affymetrix, High Wycombe, UK). Each chip was washed and stained on a GeneChipTM Fluidics Station 450 (Affymetrix, High Wycombe, UK).
| | Sample_scan_protocol | GeneChips were scanned using a GeneChipTM Scanner 450 (Affymetrix, High Wycombe, UK) employing standard recommended protocols (Affymetrix, High Wycombe, UK).
| | Sample_data_processing | The data were analyzed with analysed using R and Bioconductor packages. Data were first loaded using the affy package, followed by pre-processing (background correction, normalization and summarisation of probe level data) using the rma function.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Benard,,Kulohoma
| | Sample_contact_email | bkulohoma@iscb.org
| | Sample_contact_institute | University of Liverpool
| | Sample_contact_address | Department of Women's and Children's Health, Institute of Translational Medicine, Alder Hey Children's Hospital
| | Sample_contact_city | Liverpool
| | Sample_contact_zip/postal_code | L12 2AP
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1146nnn/GSM1146016/suppl/GSM1146016_109.CEL.gz
| | Sample_series_id | GSE47172
| | Sample_data_row_count | 22283
| | |
|
GSM1146017 | GPL96 |
|
Surviving HIV+ case replicate 2
|
Surviving HIV+ case replicate 2
|
tissue: Host peripheral blood
hiv status: HIV+
disease outcome: Alive
disease state: HIV+ case with invasive pneumococcal disease
|
Gene expression data from a surviving HIV+ case with invasive pneumococcal disease.
|
| Sample_geo_accession | GSM1146017
| | Sample_status | Public on May 23 2013
| | Sample_submission_date | May 22 2013
| | Sample_last_update_date | May 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Aliquots of 0.86 mL PAXgene™ reagent were put into 1 mL microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. The filled microtubes were stored at 80oC until analysis.
| | Sample_growth_protocol_ch1 | Whole blood was drawn at admission from consecutive children with a presumptive diagnosis of bacterial meningitis.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from whole blood using an optimised method for the PAXgene blood RNA kit (Qiagen, West Sussex, UK), according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (2mg) was reverse transcribed into double stranded cDNA using the Superscript double stranded cDNA synthesis kit (Invitrogen, Paisley, UK) according to the manufacturers’ guidelines. The double stranded cDNA was purified using a GeneChip TM sample clean-up module (Invitrogen, Paisley, UK). The purified cDNA was then biotin labelled with the ENZO BioArray high yield RNA transcript labelling kit (Affymetrix, High Wycombe, UK) and cleaned with a cRNA clean-up module (Invitrogen, Paisley, UK).
| | Sample_hyb_protocol | Aliquots of labelled cRNA (20mg) were fragmented at 94°C for 35 minutes and then hybridized to a Human Genome U133A GeneChipTM array for 16 hours rotating at 60rpm at 45°C in a GeneChipTM Hybridization Oven 640 (Affymetrix, High Wycombe, UK). Each chip was washed and stained on a GeneChipTM Fluidics Station 450 (Affymetrix, High Wycombe, UK).
| | Sample_scan_protocol | GeneChips were scanned using a GeneChipTM Scanner 450 (Affymetrix, High Wycombe, UK) employing standard recommended protocols (Affymetrix, High Wycombe, UK).
| | Sample_data_processing | The data were analyzed with analysed using R and Bioconductor packages. Data were first loaded using the affy package, followed by pre-processing (background correction, normalization and summarisation of probe level data) using the rma function.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Benard,,Kulohoma
| | Sample_contact_email | bkulohoma@iscb.org
| | Sample_contact_institute | University of Liverpool
| | Sample_contact_address | Department of Women's and Children's Health, Institute of Translational Medicine, Alder Hey Children's Hospital
| | Sample_contact_city | Liverpool
| | Sample_contact_zip/postal_code | L12 2AP
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1146nnn/GSM1146017/suppl/GSM1146017_123.CEL.gz
| | Sample_series_id | GSE47172
| | Sample_data_row_count | 22283
| | |
|
GSM1146018 | GPL96 |
|
Surviving HIV+ case replicate 3
|
Surviving HIV+ case replicate 3
|
tissue: Host peripheral blood
hiv status: HIV+
disease outcome: Alive
disease state: HIV+ case with invasive pneumococcal disease
|
Gene expression data from a surviving HIV+ case with invasive pneumococcal disease.
|
| Sample_geo_accession | GSM1146018
| | Sample_status | Public on May 23 2013
| | Sample_submission_date | May 22 2013
| | Sample_last_update_date | May 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Aliquots of 0.86 mL PAXgene™ reagent were put into 1 mL microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. The filled microtubes were stored at 80oC until analysis.
| | Sample_growth_protocol_ch1 | Whole blood was drawn at admission from consecutive children with a presumptive diagnosis of bacterial meningitis.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from whole blood using an optimised method for the PAXgene blood RNA kit (Qiagen, West Sussex, UK), according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (2mg) was reverse transcribed into double stranded cDNA using the Superscript double stranded cDNA synthesis kit (Invitrogen, Paisley, UK) according to the manufacturers’ guidelines. The double stranded cDNA was purified using a GeneChip TM sample clean-up module (Invitrogen, Paisley, UK). The purified cDNA was then biotin labelled with the ENZO BioArray high yield RNA transcript labelling kit (Affymetrix, High Wycombe, UK) and cleaned with a cRNA clean-up module (Invitrogen, Paisley, UK).
| | Sample_hyb_protocol | Aliquots of labelled cRNA (20mg) were fragmented at 94°C for 35 minutes and then hybridized to a Human Genome U133A GeneChipTM array for 16 hours rotating at 60rpm at 45°C in a GeneChipTM Hybridization Oven 640 (Affymetrix, High Wycombe, UK). Each chip was washed and stained on a GeneChipTM Fluidics Station 450 (Affymetrix, High Wycombe, UK).
| | Sample_scan_protocol | GeneChips were scanned using a GeneChipTM Scanner 450 (Affymetrix, High Wycombe, UK) employing standard recommended protocols (Affymetrix, High Wycombe, UK).
| | Sample_data_processing | The data were analyzed with analysed using R and Bioconductor packages. Data were first loaded using the affy package, followed by pre-processing (background correction, normalization and summarisation of probe level data) using the rma function.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Benard,,Kulohoma
| | Sample_contact_email | bkulohoma@iscb.org
| | Sample_contact_institute | University of Liverpool
| | Sample_contact_address | Department of Women's and Children's Health, Institute of Translational Medicine, Alder Hey Children's Hospital
| | Sample_contact_city | Liverpool
| | Sample_contact_zip/postal_code | L12 2AP
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1146nnn/GSM1146018/suppl/GSM1146018_96.CEL.gz
| | Sample_series_id | GSE47172
| | Sample_data_row_count | 22283
| | |
|
GSM1146019 | GPL96 |
|
Surviving HIV- case replicate 1
|
Surviving HIV- case replicate 1
|
tissue: Host peripheral blood
hiv status: HIV-
disease outcome: Alive
disease state: HIV- case with invasive pneumococcal disease
|
Gene expression data from a surviving HIV- case with invasive pneumococcal disease.
|
| Sample_geo_accession | GSM1146019
| | Sample_status | Public on May 23 2013
| | Sample_submission_date | May 22 2013
| | Sample_last_update_date | May 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Aliquots of 0.86 mL PAXgene™ reagent were put into 1 mL microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. The filled microtubes were stored at 80oC until analysis.
| | Sample_growth_protocol_ch1 | Whole blood was drawn at admission from consecutive children with a presumptive diagnosis of bacterial meningitis.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from whole blood using an optimised method for the PAXgene blood RNA kit (Qiagen, West Sussex, UK), according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (2mg) was reverse transcribed into double stranded cDNA using the Superscript double stranded cDNA synthesis kit (Invitrogen, Paisley, UK) according to the manufacturers’ guidelines. The double stranded cDNA was purified using a GeneChip TM sample clean-up module (Invitrogen, Paisley, UK). The purified cDNA was then biotin labelled with the ENZO BioArray high yield RNA transcript labelling kit (Affymetrix, High Wycombe, UK) and cleaned with a cRNA clean-up module (Invitrogen, Paisley, UK).
| | Sample_hyb_protocol | Aliquots of labelled cRNA (20mg) were fragmented at 94°C for 35 minutes and then hybridized to a Human Genome U133A GeneChipTM array for 16 hours rotating at 60rpm at 45°C in a GeneChipTM Hybridization Oven 640 (Affymetrix, High Wycombe, UK). Each chip was washed and stained on a GeneChipTM Fluidics Station 450 (Affymetrix, High Wycombe, UK).
| | Sample_scan_protocol | GeneChips were scanned using a GeneChipTM Scanner 450 (Affymetrix, High Wycombe, UK) employing standard recommended protocols (Affymetrix, High Wycombe, UK).
| | Sample_data_processing | The data were analyzed with analysed using R and Bioconductor packages. Data were first loaded using the affy package, followed by pre-processing (background correction, normalization and summarisation of probe level data) using the rma function.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Benard,,Kulohoma
| | Sample_contact_email | bkulohoma@iscb.org
| | Sample_contact_institute | University of Liverpool
| | Sample_contact_address | Department of Women's and Children's Health, Institute of Translational Medicine, Alder Hey Children's Hospital
| | Sample_contact_city | Liverpool
| | Sample_contact_zip/postal_code | L12 2AP
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1146nnn/GSM1146019/suppl/GSM1146019_104.CEL.gz
| | Sample_series_id | GSE47172
| | Sample_data_row_count | 22283
| | |
|
GSM1146020 | GPL96 |
|
Surviving HIV- case replicate 2
|
Surviving HIV- case replicate 2
|
tissue: Host peripheral blood
hiv status: HIV-
disease outcome: Alive
disease state: HIV- case with invasive pneumococcal disease
|
Gene expression data from a surviving HIV- case with invasive pneumococcal disease.
|
| Sample_geo_accession | GSM1146020
| | Sample_status | Public on May 23 2013
| | Sample_submission_date | May 22 2013
| | Sample_last_update_date | May 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Aliquots of 0.86 mL PAXgene™ reagent were put into 1 mL microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. The filled microtubes were stored at 80oC until analysis.
| | Sample_growth_protocol_ch1 | Whole blood was drawn at admission from consecutive children with a presumptive diagnosis of bacterial meningitis.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from whole blood using an optimised method for the PAXgene blood RNA kit (Qiagen, West Sussex, UK), according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (2mg) was reverse transcribed into double stranded cDNA using the Superscript double stranded cDNA synthesis kit (Invitrogen, Paisley, UK) according to the manufacturers’ guidelines. The double stranded cDNA was purified using a GeneChip TM sample clean-up module (Invitrogen, Paisley, UK). The purified cDNA was then biotin labelled with the ENZO BioArray high yield RNA transcript labelling kit (Affymetrix, High Wycombe, UK) and cleaned with a cRNA clean-up module (Invitrogen, Paisley, UK).
| | Sample_hyb_protocol | Aliquots of labelled cRNA (20mg) were fragmented at 94°C for 35 minutes and then hybridized to a Human Genome U133A GeneChipTM array for 16 hours rotating at 60rpm at 45°C in a GeneChipTM Hybridization Oven 640 (Affymetrix, High Wycombe, UK). Each chip was washed and stained on a GeneChipTM Fluidics Station 450 (Affymetrix, High Wycombe, UK).
| | Sample_scan_protocol | GeneChips were scanned using a GeneChipTM Scanner 450 (Affymetrix, High Wycombe, UK) employing standard recommended protocols (Affymetrix, High Wycombe, UK).
| | Sample_data_processing | The data were analyzed with analysed using R and Bioconductor packages. Data were first loaded using the affy package, followed by pre-processing (background correction, normalization and summarisation of probe level data) using the rma function.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Benard,,Kulohoma
| | Sample_contact_email | bkulohoma@iscb.org
| | Sample_contact_institute | University of Liverpool
| | Sample_contact_address | Department of Women's and Children's Health, Institute of Translational Medicine, Alder Hey Children's Hospital
| | Sample_contact_city | Liverpool
| | Sample_contact_zip/postal_code | L12 2AP
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1146nnn/GSM1146020/suppl/GSM1146020_105.CEL.gz
| | Sample_series_id | GSE47172
| | Sample_data_row_count | 22283
| | |
|
GSM1146021 | GPL96 |
|
Surviving HIV- case replicate 3
|
Surviving HIV- case replicate 3
|
tissue: Host peripheral blood
hiv status: HIV-
disease outcome: Alive
disease state: HIV- case with invasive pneumococcal disease
|
Gene expression data from a surviving HIV- case with invasive pneumococcal disease.
|
| Sample_geo_accession | GSM1146021
| | Sample_status | Public on May 23 2013
| | Sample_submission_date | May 22 2013
| | Sample_last_update_date | May 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Aliquots of 0.86 mL PAXgene™ reagent were put into 1 mL microtubes and 0.3 mL whole blood added to maintain the same recommended proportions as in the PAXgene™ evacuated tube system. The filled microtubes were stored at 80oC until analysis.
| | Sample_growth_protocol_ch1 | Whole blood was drawn at admission from consecutive children with a presumptive diagnosis of bacterial meningitis.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from whole blood using an optimised method for the PAXgene blood RNA kit (Qiagen, West Sussex, UK), according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA (2mg) was reverse transcribed into double stranded cDNA using the Superscript double stranded cDNA synthesis kit (Invitrogen, Paisley, UK) according to the manufacturers’ guidelines. The double stranded cDNA was purified using a GeneChip TM sample clean-up module (Invitrogen, Paisley, UK). The purified cDNA was then biotin labelled with the ENZO BioArray high yield RNA transcript labelling kit (Affymetrix, High Wycombe, UK) and cleaned with a cRNA clean-up module (Invitrogen, Paisley, UK).
| | Sample_hyb_protocol | Aliquots of labelled cRNA (20mg) were fragmented at 94°C for 35 minutes and then hybridized to a Human Genome U133A GeneChipTM array for 16 hours rotating at 60rpm at 45°C in a GeneChipTM Hybridization Oven 640 (Affymetrix, High Wycombe, UK). Each chip was washed and stained on a GeneChipTM Fluidics Station 450 (Affymetrix, High Wycombe, UK).
| | Sample_scan_protocol | GeneChips were scanned using a GeneChipTM Scanner 450 (Affymetrix, High Wycombe, UK) employing standard recommended protocols (Affymetrix, High Wycombe, UK).
| | Sample_data_processing | The data were analyzed with analysed using R and Bioconductor packages. Data were first loaded using the affy package, followed by pre-processing (background correction, normalization and summarisation of probe level data) using the rma function.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Benard,,Kulohoma
| | Sample_contact_email | bkulohoma@iscb.org
| | Sample_contact_institute | University of Liverpool
| | Sample_contact_address | Department of Women's and Children's Health, Institute of Translational Medicine, Alder Hey Children's Hospital
| | Sample_contact_city | Liverpool
| | Sample_contact_zip/postal_code | L12 2AP
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1146nnn/GSM1146021/suppl/GSM1146021_127.CEL.gz
| | Sample_series_id | GSE47172
| | Sample_data_row_count | 22283
| | |
|
| |
| |
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