Result

Search results for the GEO ID: GSE42853

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Title

Source name

Description

Characteristics

GSM1051319

GPL570

CMV-specific CD4 T cells, Biological Replicate 1

WRAIR* RV229

tissue: PBMC cd4 response to antigens: CMV+ hiv infection status: HIV-

Gene expression in CMV-specific CD4+ T cells, biological replicate 1

Sample_geo_accession	GSM1051319
Sample_status	Public on Dec 13 2012
Sample_submission_date	Dec 11 2012
Sample_last_update_date	Dec 13 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	PBMC cells CFSE labeled, and then divided into 3 aliquotes and stimulated by 3 different antigens: CMV, tetanux toxoid and Candida albicans for 6 day. CFSE-low, pathogen-specific CD4+ T cells from PBMC were sorted by FACS Aria.
Sample_growth_protocol_ch1	PBMC cells were maintained and cultured in complete RPMI containing 10% normal human serum (NHS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from sorted CFSE-low, CD4 cells using RNeasy Plus Mini Kit (Qiagen).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA reverse transcription and synthesis of biotin-labeled aRNA were performed using GeneChip IVT Express Kit (Affymetrix).
Sample_hyb_protocol	Standard hybridization protocol
Sample_scan_protocol	Standard scanning protocol
Sample_data_processing	Data processing and analysis were performed using the R computing environment version 2.12.2 with BioConductor packages.
Sample_data_processing	Gene expression data were normalized into Robust Multichip Average expression measures21 and were compared between antigen specificities (CMV vs. combined TT and Candida). False discovery rate (FDR) or the expected proportion of false positives among all significant genes was estimated based on SAM scores.
Sample_platform_id	GPL570
Sample_contact_name	Haitao,,Hu
Sample_contact_email	hhu@hivresearch.org
Sample_contact_phone	301-319-3012
Sample_contact_department	US Military HIV Research Program
Sample_contact_institute	Walter Reed Army Institute of Research
Sample_contact_address	503 Robert Grant Ave
Sample_contact_city	Silver Spring
Sample_contact_state	MD
Sample_contact_zip/postal_code	20910
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051319/suppl/GSM1051319_HU-RV229-060.CMV.CFSE-Lo.CEL.gz
Sample_series_id	GSE42853
Sample_data_row_count	54675

GSM1051320

GPL570

TT-specific CD4 T cells, Biological Replicate 1

WRAIR* RV229

tissue: PBMC cd4 response to antigens: Tetanus toxoid+ hiv infection status: HIV-

Gene expression in TT-specific CD4+ T cells, biological replicate 1

Sample_geo_accession	GSM1051320
Sample_status	Public on Dec 13 2012
Sample_submission_date	Dec 11 2012
Sample_last_update_date	Dec 13 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	PBMC cells CFSE labeled, and then divided into 3 aliquotes and stimulated by 3 different antigens: CMV, tetanux toxoid and Candida albicans for 6 day. CFSE-low, pathogen-specific CD4+ T cells from PBMC were sorted by FACS Aria.
Sample_growth_protocol_ch1	PBMC cells were maintained and cultured in complete RPMI containing 10% normal human serum (NHS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from sorted CFSE-low, CD4 cells using RNeasy Plus Mini Kit (Qiagen).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA reverse transcription and synthesis of biotin-labeled aRNA were performed using GeneChip IVT Express Kit (Affymetrix).
Sample_hyb_protocol	Standard hybridization protocol
Sample_scan_protocol	Standard scanning protocol
Sample_data_processing	Data processing and analysis were performed using the R computing environment version 2.12.2 with BioConductor packages.
Sample_data_processing	Gene expression data were normalized into Robust Multichip Average expression measures21 and were compared between antigen specificities (CMV vs. combined TT and Candida). False discovery rate (FDR) or the expected proportion of false positives among all significant genes was estimated based on SAM scores.
Sample_platform_id	GPL570
Sample_contact_name	Haitao,,Hu
Sample_contact_email	hhu@hivresearch.org
Sample_contact_phone	301-319-3012
Sample_contact_department	US Military HIV Research Program
Sample_contact_institute	Walter Reed Army Institute of Research
Sample_contact_address	503 Robert Grant Ave
Sample_contact_city	Silver Spring
Sample_contact_state	MD
Sample_contact_zip/postal_code	20910
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051320/suppl/GSM1051320_HU-RV229-060.TT.CFSE-Lo.CEL.gz
Sample_series_id	GSE42853
Sample_data_row_count	54675

GSM1051321

GPL570

Candida-specific CD4 T cells, Biological Replicate 1

WRAIR* RV229

tissue: PBMC cd4 response to antigens: Candida Albicans+ hiv infection status: HIV-

Gene expression in Candida-specific CD4+ T cells, biological replicate 1

Sample_geo_accession	GSM1051321
Sample_status	Public on Dec 13 2012
Sample_submission_date	Dec 11 2012
Sample_last_update_date	Dec 13 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	PBMC cells CFSE labeled, and then divided into 3 aliquotes and stimulated by 3 different antigens: CMV, tetanux toxoid and Candida albicans for 6 day. CFSE-low, pathogen-specific CD4+ T cells from PBMC were sorted by FACS Aria.
Sample_growth_protocol_ch1	PBMC cells were maintained and cultured in complete RPMI containing 10% normal human serum (NHS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from sorted CFSE-low, CD4 cells using RNeasy Plus Mini Kit (Qiagen).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA reverse transcription and synthesis of biotin-labeled aRNA were performed using GeneChip IVT Express Kit (Affymetrix).
Sample_hyb_protocol	Standard hybridization protocol
Sample_scan_protocol	Standard scanning protocol
Sample_data_processing	Data processing and analysis were performed using the R computing environment version 2.12.2 with BioConductor packages.
Sample_data_processing	Gene expression data were normalized into Robust Multichip Average expression measures21 and were compared between antigen specificities (CMV vs. combined TT and Candida). False discovery rate (FDR) or the expected proportion of false positives among all significant genes was estimated based on SAM scores.
Sample_platform_id	GPL570
Sample_contact_name	Haitao,,Hu
Sample_contact_email	hhu@hivresearch.org
Sample_contact_phone	301-319-3012
Sample_contact_department	US Military HIV Research Program
Sample_contact_institute	Walter Reed Army Institute of Research
Sample_contact_address	503 Robert Grant Ave
Sample_contact_city	Silver Spring
Sample_contact_state	MD
Sample_contact_zip/postal_code	20910
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051321/suppl/GSM1051321_HU-RV229-060.Candida.CFSE-Lo.CEL.gz
Sample_series_id	GSE42853
Sample_data_row_count	54675

GSM1051322

GPL570

CMV-specific CD4 T cells, Biological Replicate 2

WRAIR* RV229

tissue: PBMC cd4 response to antigens: CMV+ hiv infection status: HIV-

Gene expression in CMV-specific CD4+ T cells, biological replicate 2

Sample_geo_accession	GSM1051322
Sample_status	Public on Dec 13 2012
Sample_submission_date	Dec 11 2012
Sample_last_update_date	Dec 13 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	PBMC cells CFSE labeled, and then divided into 3 aliquotes and stimulated by 3 different antigens: CMV, tetanux toxoid and Candida albicans for 6 day. CFSE-low, pathogen-specific CD4+ T cells from PBMC were sorted by FACS Aria.
Sample_growth_protocol_ch1	PBMC cells were maintained and cultured in complete RPMI containing 10% normal human serum (NHS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from sorted CFSE-low, CD4 cells using RNeasy Plus Mini Kit (Qiagen).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA reverse transcription and synthesis of biotin-labeled aRNA were performed using GeneChip IVT Express Kit (Affymetrix).
Sample_hyb_protocol	Standard hybridization protocol
Sample_scan_protocol	Standard scanning protocol
Sample_data_processing	Data processing and analysis were performed using the R computing environment version 2.12.2 with BioConductor packages.
Sample_data_processing	Gene expression data were normalized into Robust Multichip Average expression measures21 and were compared between antigen specificities (CMV vs. combined TT and Candida). False discovery rate (FDR) or the expected proportion of false positives among all significant genes was estimated based on SAM scores.
Sample_platform_id	GPL570
Sample_contact_name	Haitao,,Hu
Sample_contact_email	hhu@hivresearch.org
Sample_contact_phone	301-319-3012
Sample_contact_department	US Military HIV Research Program
Sample_contact_institute	Walter Reed Army Institute of Research
Sample_contact_address	503 Robert Grant Ave
Sample_contact_city	Silver Spring
Sample_contact_state	MD
Sample_contact_zip/postal_code	20910
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051322/suppl/GSM1051322_HU-RV229-080.CMV.CFSE-Lo.CEL.gz
Sample_series_id	GSE42853
Sample_data_row_count	54675

GSM1051323

GPL570

TT-specific CD4 T cells, Biological Replicate 2

WRAIR* RV229

tissue: PBMC cd4 response to antigens: Tetanus toxoid+ hiv infection status: HIV-

Gene expression in TT-specific CD4+ T cells, biological replicate 2

Sample_geo_accession	GSM1051323
Sample_status	Public on Dec 13 2012
Sample_submission_date	Dec 11 2012
Sample_last_update_date	Dec 13 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	PBMC cells CFSE labeled, and then divided into 3 aliquotes and stimulated by 3 different antigens: CMV, tetanux toxoid and Candida albicans for 6 day. CFSE-low, pathogen-specific CD4+ T cells from PBMC were sorted by FACS Aria.
Sample_growth_protocol_ch1	PBMC cells were maintained and cultured in complete RPMI containing 10% normal human serum (NHS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from sorted CFSE-low, CD4 cells using RNeasy Plus Mini Kit (Qiagen).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA reverse transcription and synthesis of biotin-labeled aRNA were performed using GeneChip IVT Express Kit (Affymetrix).
Sample_hyb_protocol	Standard hybridization protocol
Sample_scan_protocol	Standard scanning protocol
Sample_data_processing	Data processing and analysis were performed using the R computing environment version 2.12.2 with BioConductor packages.
Sample_data_processing	Gene expression data were normalized into Robust Multichip Average expression measures21 and were compared between antigen specificities (CMV vs. combined TT and Candida). False discovery rate (FDR) or the expected proportion of false positives among all significant genes was estimated based on SAM scores.
Sample_platform_id	GPL570
Sample_contact_name	Haitao,,Hu
Sample_contact_email	hhu@hivresearch.org
Sample_contact_phone	301-319-3012
Sample_contact_department	US Military HIV Research Program
Sample_contact_institute	Walter Reed Army Institute of Research
Sample_contact_address	503 Robert Grant Ave
Sample_contact_city	Silver Spring
Sample_contact_state	MD
Sample_contact_zip/postal_code	20910
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051323/suppl/GSM1051323_HU-RV229-080.TT.CFSE-Lo.CEL.gz
Sample_series_id	GSE42853
Sample_data_row_count	54675

GSM1051324

GPL570

Candida-specific CD4 T cells, Biological Replicate 2

WRAIR* RV229

tissue: PBMC cd4 response to antigens: Candida Albicans+ hiv infection status: HIV-

Gene expression in Candida-specific CD4+ T cells, biological replicate 2

Sample_geo_accession	GSM1051324
Sample_status	Public on Dec 13 2012
Sample_submission_date	Dec 11 2012
Sample_last_update_date	Dec 13 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	PBMC cells CFSE labeled, and then divided into 3 aliquotes and stimulated by 3 different antigens: CMV, tetanux toxoid and Candida albicans for 6 day. CFSE-low, pathogen-specific CD4+ T cells from PBMC were sorted by FACS Aria.
Sample_growth_protocol_ch1	PBMC cells were maintained and cultured in complete RPMI containing 10% normal human serum (NHS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from sorted CFSE-low, CD4 cells using RNeasy Plus Mini Kit (Qiagen).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA reverse transcription and synthesis of biotin-labeled aRNA were performed using GeneChip IVT Express Kit (Affymetrix).
Sample_hyb_protocol	Standard hybridization protocol
Sample_scan_protocol	Standard scanning protocol
Sample_data_processing	Data processing and analysis were performed using the R computing environment version 2.12.2 with BioConductor packages.
Sample_data_processing	Gene expression data were normalized into Robust Multichip Average expression measures21 and were compared between antigen specificities (CMV vs. combined TT and Candida). False discovery rate (FDR) or the expected proportion of false positives among all significant genes was estimated based on SAM scores.
Sample_platform_id	GPL570
Sample_contact_name	Haitao,,Hu
Sample_contact_email	hhu@hivresearch.org
Sample_contact_phone	301-319-3012
Sample_contact_department	US Military HIV Research Program
Sample_contact_institute	Walter Reed Army Institute of Research
Sample_contact_address	503 Robert Grant Ave
Sample_contact_city	Silver Spring
Sample_contact_state	MD
Sample_contact_zip/postal_code	20910
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051324/suppl/GSM1051324_HU-RV229-080.Candida.CFSE-Lo.CEL.gz
Sample_series_id	GSE42853
Sample_data_row_count	54675

GSM1051325

GPL570

CMV-specific CD4 T cells, Biological Replicate 3

WRAIR* RV229

tissue: PBMC cd4 response to antigens: CMV+ hiv infection status: HIV-

Gene expression in CMV-specific CD4+ T cells, biological replicate 3

Sample_geo_accession	GSM1051325
Sample_status	Public on Dec 13 2012
Sample_submission_date	Dec 11 2012
Sample_last_update_date	Dec 13 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	PBMC cells CFSE labeled, and then divided into 3 aliquotes and stimulated by 3 different antigens: CMV, tetanux toxoid and Candida albicans for 6 day. CFSE-low, pathogen-specific CD4+ T cells from PBMC were sorted by FACS Aria.
Sample_growth_protocol_ch1	PBMC cells were maintained and cultured in complete RPMI containing 10% normal human serum (NHS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from sorted CFSE-low, CD4 cells using RNeasy Plus Mini Kit (Qiagen).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA reverse transcription and synthesis of biotin-labeled aRNA were performed using GeneChip IVT Express Kit (Affymetrix).
Sample_hyb_protocol	Standard hybridization protocol
Sample_scan_protocol	Standard scanning protocol
Sample_data_processing	Data processing and analysis were performed using the R computing environment version 2.12.2 with BioConductor packages.
Sample_data_processing	Gene expression data were normalized into Robust Multichip Average expression measures21 and were compared between antigen specificities (CMV vs. combined TT and Candida). False discovery rate (FDR) or the expected proportion of false positives among all significant genes was estimated based on SAM scores.
Sample_platform_id	GPL570
Sample_contact_name	Haitao,,Hu
Sample_contact_email	hhu@hivresearch.org
Sample_contact_phone	301-319-3012
Sample_contact_department	US Military HIV Research Program
Sample_contact_institute	Walter Reed Army Institute of Research
Sample_contact_address	503 Robert Grant Ave
Sample_contact_city	Silver Spring
Sample_contact_state	MD
Sample_contact_zip/postal_code	20910
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051325/suppl/GSM1051325_HU-RV229-144.CMV.CFSE-Lo.CEL.gz
Sample_series_id	GSE42853
Sample_data_row_count	54675

GSM1051326

GPL570

TT-specific CD4 T cells, Biological Replicate 3

WRAIR* RV229

tissue: PBMC cd4 response to antigens: Tetanus toxoid+ hiv infection status: HIV-

Gene expression in TT-specific CD4+ T cells, biological replicate 3

Sample_geo_accession	GSM1051326
Sample_status	Public on Dec 13 2012
Sample_submission_date	Dec 11 2012
Sample_last_update_date	Dec 13 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	PBMC cells CFSE labeled, and then divided into 3 aliquotes and stimulated by 3 different antigens: CMV, tetanux toxoid and Candida albicans for 6 day. CFSE-low, pathogen-specific CD4+ T cells from PBMC were sorted by FACS Aria.
Sample_growth_protocol_ch1	PBMC cells were maintained and cultured in complete RPMI containing 10% normal human serum (NHS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from sorted CFSE-low, CD4 cells using RNeasy Plus Mini Kit (Qiagen).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA reverse transcription and synthesis of biotin-labeled aRNA were performed using GeneChip IVT Express Kit (Affymetrix).
Sample_hyb_protocol	Standard hybridization protocol
Sample_scan_protocol	Standard scanning protocol
Sample_data_processing	Data processing and analysis were performed using the R computing environment version 2.12.2 with BioConductor packages.
Sample_data_processing	Gene expression data were normalized into Robust Multichip Average expression measures21 and were compared between antigen specificities (CMV vs. combined TT and Candida). False discovery rate (FDR) or the expected proportion of false positives among all significant genes was estimated based on SAM scores.
Sample_platform_id	GPL570
Sample_contact_name	Haitao,,Hu
Sample_contact_email	hhu@hivresearch.org
Sample_contact_phone	301-319-3012
Sample_contact_department	US Military HIV Research Program
Sample_contact_institute	Walter Reed Army Institute of Research
Sample_contact_address	503 Robert Grant Ave
Sample_contact_city	Silver Spring
Sample_contact_state	MD
Sample_contact_zip/postal_code	20910
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051326/suppl/GSM1051326_HU-RV229-144.TT.CFSE-Lo.CEL.gz
Sample_series_id	GSE42853
Sample_data_row_count	54675

GSM1051327

GPL570

Candida-specific CD4 T cells, Biological Replicate 3

WRAIR* RV229

tissue: PBMC cd4 response to antigens: Candida Albicans+ hiv infection status: HIV-

Gene expression in Candida-specific CD4+ T cells, biological replicate 3

Sample_geo_accession	GSM1051327
Sample_status	Public on Dec 13 2012
Sample_submission_date	Dec 11 2012
Sample_last_update_date	Dec 13 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	PBMC cells CFSE labeled, and then divided into 3 aliquotes and stimulated by 3 different antigens: CMV, tetanux toxoid and Candida albicans for 6 day. CFSE-low, pathogen-specific CD4+ T cells from PBMC were sorted by FACS Aria.
Sample_growth_protocol_ch1	PBMC cells were maintained and cultured in complete RPMI containing 10% normal human serum (NHS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from sorted CFSE-low, CD4 cells using RNeasy Plus Mini Kit (Qiagen).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA reverse transcription and synthesis of biotin-labeled aRNA were performed using GeneChip IVT Express Kit (Affymetrix).
Sample_hyb_protocol	Standard hybridization protocol
Sample_scan_protocol	Standard scanning protocol
Sample_data_processing	Data processing and analysis were performed using the R computing environment version 2.12.2 with BioConductor packages.
Sample_data_processing	Gene expression data were normalized into Robust Multichip Average expression measures21 and were compared between antigen specificities (CMV vs. combined TT and Candida). False discovery rate (FDR) or the expected proportion of false positives among all significant genes was estimated based on SAM scores.
Sample_platform_id	GPL570
Sample_contact_name	Haitao,,Hu
Sample_contact_email	hhu@hivresearch.org
Sample_contact_phone	301-319-3012
Sample_contact_department	US Military HIV Research Program
Sample_contact_institute	Walter Reed Army Institute of Research
Sample_contact_address	503 Robert Grant Ave
Sample_contact_city	Silver Spring
Sample_contact_state	MD
Sample_contact_zip/postal_code	20910
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051327/suppl/GSM1051327_HU-RV229-144.Candida.CFSE-Lo.CEL.gz
Sample_series_id	GSE42853
Sample_data_row_count	54675

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