Sample Set Annotation Tool: Human blood monocyte profile in Ventilator-Associated Pneumonia patients-GSE12838

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Hypothesis

The informational content of circulating leukocytes differs, thereby allowing one to rank leukocyte populations on their potential to contribute to RNA diagnostics for pneumonia.

Experimental Design

Four patients over several timepoints measured three different cell types for VAP signal

Experimental Variables

Controls

Methods

Sixteen patients (10 male, 6 female) at risk for VAP were entered into our IRB-approved study that collects blood and clinical data every 48 hours for up to 21 days. Four of the sixteen patients developed VAP as diagnosed and treated by the attending ICU physician. Previously reported blood protocols were used to isolate buffy coat, enriched neutrophil, and enriched monocyte populations by using negative selection. Cellular purity was assessed by FACS for one of the 4 VAP patients. Genome-wide expression analysis was performed on RMA-normalized signal from Affymetrix U133 2.0 Plus GeneChips. EDGE software (FDR=0.10) was used to determine changes in mRNA abundance over time for each cell population.

Additional Information

Cobb JP, Schierding W, Dixon D, Ruan J, Oppedal D, MacMillan S, Brownstein B, Zhang W

Expected Samples:

60 Samples Loaded: 60

Species

Human (Homo sapiens)

Sample Source

Neutrophils , Monocytes

Disease

Pneumonia

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	Age	Donor ID	Ethnicity	!Sample_title	Gender
GSM322246	33	41	Caucasian	Buffycoat_patient41_time1	Male,Ethnicity:Caucasian,Age:33,VAP day:5
GSM322247	33	41	Caucasian	Buffycoat_patient41_time11	Male,Ethnicity:Caucasian,Age:33,VAP day:5
GSM322248	33	41	Caucasian	Buffycoat_patient41_time3	Male,Ethnicity:Caucasian,Age:33,VAP day:5
GSM322249	33	41	Caucasian	Buffycoat_patient41_time5	Male,Ethnicity:Caucasian,Age:33,VAP day:5
GSM322250	33	41	Caucasian	Buffycoat_patient41_time7	Male,Ethnicity:Caucasian,Age:33,VAP day:5

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File
sampleset4000088_sampleannotations.csv Sample Set Spreadsheet

Samples Viewer / Editor

All fields are editable except the "Sample ID" column. To edit a cell, click within the cell. To edit a "date" cell, click on the calendar icon. To cancel an edit, press the ESC key.

Sample ID	Age	Donor ID	Ethnicity	!Sample Title	Gender	Cell type	Time of blood collection	Sex	Day of VAP	Cell type and VAP
GSM322246	33	41	Caucasian	Buffycoat_patient41_time1	Male,Ethnicity:Caucasian,Age:33,VAP day:5	Buffycoat	1	Male	5	Buffy Day 5
GSM322247	33	41	Caucasian	Buffycoat_patient41_time11	Male,Ethnicity:Caucasian,Age:33,VAP day:5	Buffycoat	11	Male	5	Buffy Day 5
GSM322248	33	41	Caucasian	Buffycoat_patient41_time3	Male,Ethnicity:Caucasian,Age:33,VAP day:5	Buffycoat	3	Male	5	Buffy Day 5
GSM322249	33	41	Caucasian	Buffycoat_patient41_time5	Male,Ethnicity:Caucasian,Age:33,VAP day:5	Buffycoat	5	Male	5	Buffy Day 5
GSM322250	33	41	Caucasian	Buffycoat_patient41_time7	Male,Ethnicity:Caucasian,Age:33,VAP day:5	Buffycoat	7	Male	5	Buffy Day 5
GSM322251	33	41	Caucasian	Buffycoat_patient41_time9	Male,Ethnicity:Caucasian,Age:33,VAP day:5	Buffycoat	9	Male	5	Buffy Day 5
GSM322252	32	45	African-american	Buffycoat_patient45_time1	Male,Ethnicity:African-american,Age:32,VAP day:3	Buffycoat	1	Male	3	Buffy Day 3
GSM322253	32	45	African-american	Buffycoat_patient45_time3	Male,Ethnicity:African-american,Age:32,VAP day:3	Buffycoat	3	Male	3	Buffy Day 3
GSM322254	32	45	African-american	Buffycoat_patient45_time5	Male,Ethnicity:African-american,Age:32,VAP day:3	Buffycoat	5	Male	3	Buffy Day 3
GSM322255	32	45	African-american	Buffycoat_patient45_time7	Male,Ethnicity:African-american,Age:32,VAP day:3	Buffycoat	7	Male	3	Buffy Day 3
GSM322256	32	45	African-american	Buffycoat_patient45_time9	Male,Ethnicity:African-american,Age:32,VAP day:3	Buffycoat	9	Male	3	Buffy Day 3
GSM322257	59	50	Caucasian	Buffycoat_patient50_time1	Male,Ethnicity:Caucasian,Age:59,VAP day:7	Buffycoat	1	Male	7	Buffy Day 7
GSM322258	59	50	Caucasian	Buffycoat_patient50_time11	Male,Ethnicity:Caucasian,Age:59,VAP day:7	Buffycoat	11	Male	7	Buffy Day 7
GSM322259	59	50	Caucasian	Buffycoat_patient50_time3	Male,Ethnicity:Caucasian,Age:59,VAP day:7	Buffycoat	3	Male	7	Buffy Day 7
GSM322260	59	50	Caucasian	Buffycoat_patient50_time5	Male,Ethnicity:Caucasian,Age:59,VAP day:7	Buffycoat	5	Male	7	Buffy Day 7
GSM322261	59	50	Caucasian	Buffycoat_patient50_time7	Male,Ethnicity:Caucasian,Age:59,VAP day:7	Buffycoat	7	Male	7	Buffy Day 7
GSM322262	59	50	Caucasian	Buffycoat_patient50_time9	Male,Ethnicity:Caucasian,Age:59,VAP day:7	Buffycoat	9	Male	7	Buffy Day 7
GSM322263	46	51	African-american	Buffycoat_patient51_time1	Male,Ethnicity:African-american,Age:46,VAP day:3	Buffycoat	1	Male	3	Buffy Day 3
GSM322264	46	51	African-american	Buffycoat_patient51_time3	Male,Ethnicity:African-american,Age:46,VAP day:3	Buffycoat	3	Male	3	Buffy Day 3
GSM322265	46	51	African-american	Buffycoat_patient51_time5	Male,Ethnicity:African-american,Age:46,VAP day:3	Buffycoat	5	Male	3	Buffy Day 3
GSM322266	46	51	African-american	Buffycoat_patient51_time7	Male,Ethnicity:African-american,Age:46,VAP day:3	Buffycoat	7	Male	3	Buffy Day 3
GSM322267	46	51	African-american	Buffycoat_patient51_time9	Male,Ethnicity:African-american,Age:46,VAP day:3	Buffycoat	9	Male	3	Buffy Day 3
GSM322268	33	41	Caucasian	Monocyte_patient41_time3	Male,Ethnicity:Caucasian,Age:33,VAP day:5	Monocyte	3	Male	5	Mono Day 5
GSM322269	33	41	Caucasian	Monocyte_patient41_time7	Male,Ethnicity:Caucasian,Age:33,VAP day:5	Monocyte	7	Male	5	Mono Day 5
GSM322270	33	41	Caucasian	Monocyte_patient41_time9	Male,Ethnicity:Caucasian,Age:33,VAP day:5	Monocyte	9	Male	5	Mono Day 5
GSM322271	33	41	Caucasian	Monocyte_patient41_time11	Male,Ethnicity:Caucasian,Age:33,VAP day:5	Monocyte	11	Male	5	Mono Day 5
GSM322272	33	41	Caucasian	Monocyte_patient41_time1	Male,Ethnicity:Caucasian,Age:33,VAP day:5	Monocyte	1	Male	5	Mono Day 5
GSM322273	32	45	African-american	Monocyte_patient45_time1	Male,Ethnicity:African-american,Age:32,VAP day:3	Monocyte	1	Male	3	Mono Day 3
GSM322274	32	45	African-american	Monocyte_patient45_time3	Male,Ethnicity:African-american,Age:32,VAP day:3	Monocyte	3	Male	3	Mono Day 3
GSM322275	32	45	African-american	Monocyte_patient45_time5	Male,Ethnicity:African-american,Age:32,VAP day:3	Monocyte	5	Male	3	Mono Day 3
GSM322276	32	45	African-american	Monocyte_patient45_time7	Male,Ethnicity:African-american,Age:32,VAP day:3	Monocyte	7	Male	3	Mono Day 3
GSM322277	32	45	African-american	Monocyte_patient45_time9	Male,Ethnicity:African-american,Age:32,VAP day:3	Monocyte	9	Male	3	Mono Day 3
GSM322278	59	50	Caucasian	Monocyte_patient50_time1	Male,Ethnicity:Caucasian,Age:59,VAP day:7	Monocyte	1	Male	7	Mono Day 7
GSM322279	59	50	Caucasian	Monocyte_patient50_time3	Male,Ethnicity:Caucasian,Age:59,VAP day:7	Monocyte	3	Male	7	Mono Day 7
GSM322280	59	50	Caucasian	Monocyte_patient50_time5	Male,Ethnicity:Caucasian,Age:59,VAP day:7	Monocyte	5	Male	7	Mono Day 7
GSM322281	59	50	Caucasian	Monocyte_patient50_time7	Male,Ethnicity:Caucasian,Age:59,VAP day:7	Monocyte	7	Male	7	Mono Day 7
GSM322282	59	50	Caucasian	Monocyte_patient50_time9	Male,Ethnicity:Caucasian,Age:59,VAP day:7	Monocyte	9	Male	7	Mono Day 7
GSM322283	46	51	African-american	Monocyte_patient51_time5	Male,Ethnicity:African-american,Age:46,VAP day:3	Monocyte	5	Male	3	Mono Day 3
GSM322284	46	51	African-american	Monocyte_patient51_time7	Male,Ethnicity:African-american,Age:46,VAP day:3	Monocyte	7	Male	3	Mono Day 3
GSM322285	46	51	African-american	Monocyte_patient51_time9	Male,Ethnicity:African-american,Age:46,VAP day:3	Monocyte	9	Male	3	Mono Day 3
GSM322286	33	41	Caucasian	Neutrophil_patient41_time3	Male,Ethnicity:Caucasian,Age:33,VAP day:5	Neutrophil	3	Male	5	Neutro Day 5
GSM322287	33	41	Caucasian	Neutrophil_patient41_time7	Male,Ethnicity:Caucasian,Age:33,VAP day:5	Neutrophil	7	Male	5	Neutro Day 5
GSM322288	33	41	Caucasian	Neutrophil_patient41_time9	Male,Ethnicity:Caucasian,Age:33,VAP day:5	Neutrophil	9	Male	5	Neutro Day 5
GSM322289	33	41	Caucasian	Neutrophil_patient41_time11	Male,Ethnicity:Caucasian,Age:33,VAP day:5	Neutrophil	11	Male	5	Neutro Day 5
GSM322290	33	41	Caucasian	Neutrophil_patient41_time1	Male,Ethnicity:Caucasian,Age:33,VAP day:5	Neutrophil	1	Male	5	Neutro Day 5
GSM322291	32	45	African-american	Neutrophil_patient45_time1	Male,Ethnicity:African-american,Age:32,VAP day:3	Neutrophil	1	Male	3	Neutro Day 3
GSM322292	32	45	African-american	Neutrophil_patient45_time3	Male,Ethnicity:African-american,Age:32,VAP day:3	Neutrophil	3	Male	3	Neutro Day 3
GSM322293	32	45	African-american	Neutrophil_patient45_time5	Male,Ethnicity:African-american,Age:32,VAP day:3	Neutrophil	5	Male	3	Neutro Day 3
GSM322294	32	45	African-american	Neutrophil_patient45_time7	Male,Ethnicity:African-american,Age:32,VAP day:3	Neutrophil	7	Male	3	Neutro Day 3
GSM322295	32	45	African-american	Neutrophil_patient45_time9	Male,Ethnicity:African-american,Age:32,VAP day:3	Neutrophil	9	Male	3	Neutro Day 3
GSM322296	59	50	Caucasian	Neutrophil_patient50_time3	Male,Ethnicity:Caucasian,Age:59,VAP day:7	Neutrophil	3	Male	7	Neutro Day 7
GSM322297	59	50	Caucasian	Neutrophil_patient50_time5	Male,Ethnicity:Caucasian,Age:59,VAP day:7	Neutrophil	5	Male	7	Neutro Day 7
GSM322298	59	50	Caucasian	Neutrophil_patient50_time7	Male,Ethnicity:Caucasian,Age:59,VAP day:7	Neutrophil	7	Male	7	Neutro Day 7
GSM322299	59	50	Caucasian	Neutrophil_patient50_time9	Male,Ethnicity:Caucasian,Age:59,VAP day:7	Neutrophil	9	Male	7	Neutro Day 7
GSM322300	59	50	Caucasian	Neutrophil_patient50_time11	Male,Ethnicity:Caucasian,Age:59,VAP day:7	Neutrophil	11	Male	7	Neutro Day 7
GSM322301	46	51	African-american	Neutrophil_patient51_time1	Male,Ethnicity:African-american,Age:46,VAP day:3	Neutrophil	1	Male	3	Neutro Day 3
GSM322302	46	51	African-american	Neutrophil_patient51_time3	Male,Ethnicity:African-american,Age:46,VAP day:3	Neutrophil	3	Male	3	Neutro Day 3
GSM322303	46	51	African-american	Neutrophil_patient51_time5	Male,Ethnicity:African-american,Age:46,VAP day:3	Neutrophil	5	Male	3	Neutro Day 3
GSM322304	46	51	African-american	Neutrophil_patient51_time7	Male,Ethnicity:African-american,Age:46,VAP day:3	Neutrophil	7	Male	3	Neutro Day 3
GSM322305	46	51	African-american	Neutrophil_patient51_time9	Male,Ethnicity:African-american,Age:46,VAP day:3	Neutrophil	9	Male	3	Neutro Day 3

Group Sets View in Gene Expression Browser

Name
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Module Analysis

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Cell Type
Cell Type and VAP

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