Result

Search results for the GEO ID: GSE23183

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM570762

GPL570

Patient 1

Blood from an HIV-1 infected adolescent boy

developmental stage: adolescent sex: male cell type: peripheral blood mononuclear cells hiv disease status: soluble CD8-suppression

Sample_geo_accession	GSM570762
Sample_status	Public on Oct 28 2010
Sample_submission_date	Jul 27 2010
Sample_last_update_date	Jul 28 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Five x 106 – 107 peripheral blood mononuclear cells were viably-frozen using RNAlater ([Ambion]; to maximize RNA extraction) at the same time the suppression assays were performed. RNA extraction (using the Qiagen RNeasy mini kit) was performed 5-10 months after the cell pellets were frozen.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Extracted RNA was reverse transcribed to form double stranded DNA (Invitrogen SuperScript Choice), purified over phenol-chloroform and concentrated via ethanol-precipitation. Biotin-labeled cRNA was then in vitro transcribed (BioArray High-Yield in vitro RNA transcription and labeling kit [Affymetrix]), purified (Qiagen RNeasy spin columns) and fragmented.
Sample_hyb_protocol	Fragmented RNA was then hybridized onto the Affymetrix Human Genome U 133 Plus 2.0 array, according to the manufacturer’s recommendations (Gene Chip RHT One-Cycle Target Labeling).
Sample_scan_protocol	An automatic fluidic station washed, stained and scanned the sample for fluorescence using an Affymetrix GCS3000 scanner.
Sample_data_processing	The data were analyzed using the average difference values followed by the quantile normalization procedure and absolute calls for the presence or absence of the genes present on the chip in Bioconductor package : affy using R software (version 2.8).
Sample_data_processing	We compared those genes differentially expressed at least two-fold by Patient 1 who demonstrated soluble CD8-suppression with those genes from Patient 2 who exhibited no suppression and analyzed those results based on previous reports in the literature as to what might constitute CAF using the proportion test and what might be expected to be seen in exosomes secreted by CD8+ T-cells. We then compared the gene expression profile of Patient 3 (who exhibited suppression of HIV likely via direct contact, and thus unrelated to CAF) with that of Patients 1 and 2 using Pearson correlation coefficients. Results of differentially expressed gene analysis is provided as a supplementary file on the Series record.
Sample_platform_id	GPL570
Sample_contact_name	Ben,,Katz
Sample_contact_email	BKatz@childrensmemorial.org
Sample_contact_phone	773-880-4187
Sample_contact_fax	773-880-8226
Sample_contact_department	Division of Infectious Diseases
Sample_contact_institute	Children's Memorial Hospital
Sample_contact_address	2300 Children's Plaza, Box # 20
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60614
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM570nnn/GSM570762/suppl/GSM570762.CEL.gz
Sample_series_id	GSE23183
Sample_data_row_count	54675

GSM570764

GPL570

Patient 3

Blood from an HIV-1 infected adolescent boy

developmental stage: adolescent sex: male cell type: peripheral blood mononuclear cells hiv disease status: HIV suppression likely via direct contact (unrelated to CAF)

Sample_geo_accession	GSM570764
Sample_status	Public on Oct 28 2010
Sample_submission_date	Jul 27 2010
Sample_last_update_date	Jul 28 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Five x 106 – 107 peripheral blood mononuclear cells were viably-frozen using RNAlater ([Ambion]; to maximize RNA extraction) at the same time the suppression assays were performed. RNA extraction (using the Qiagen RNeasy mini kit) was performed 5-10 months after the cell pellets were frozen.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Extracted RNA was reverse transcribed to form double stranded DNA (Invitrogen SuperScript Choice), purified over phenol-chloroform and concentrated via ethanol-precipitation. Biotin-labeled cRNA was then in vitro transcribed (BioArray High-Yield in vitro RNA transcription and labeling kit [Affymetrix]), purified (Qiagen RNeasy spin columns) and fragmented.
Sample_hyb_protocol	Fragmented RNA was then hybridized onto the Affymetrix Human Genome U 133 Plus 2.0 array, according to the manufacturer’s recommendations (Gene Chip RHT One-Cycle Target Labeling).
Sample_scan_protocol	An automatic fluidic station washed, stained and scanned the sample for fluorescence using an Affymetrix GCS3000 scanner.
Sample_data_processing	The data were analyzed using the average difference values followed by the quantile normalization procedure and absolute calls for the presence or absence of the genes present on the chip in Bioconductor package : affy using R software (version 2.8).
Sample_data_processing	We compared those genes differentially expressed at least two-fold by Patient 1 who demonstrated soluble CD8-suppression with those genes from Patient 2 who exhibited no suppression and analyzed those results based on previous reports in the literature as to what might constitute CAF using the proportion test and what might be expected to be seen in exosomes secreted by CD8+ T-cells. We then compared the gene expression profile of Patient 3 (who exhibited suppression of HIV likely via direct contact, and thus unrelated to CAF) with that of Patients 1 and 2 using Pearson correlation coefficients. Results of differentially expressed gene analysis is provided as a supplementary file on the Series record.
Sample_platform_id	GPL570
Sample_contact_name	Ben,,Katz
Sample_contact_email	BKatz@childrensmemorial.org
Sample_contact_phone	773-880-4187
Sample_contact_fax	773-880-8226
Sample_contact_department	Division of Infectious Diseases
Sample_contact_institute	Children's Memorial Hospital
Sample_contact_address	2300 Children's Plaza, Box # 20
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60614
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM570nnn/GSM570764/suppl/GSM570764.CEL.gz
Sample_series_id	GSE23183
Sample_data_row_count	54675

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