Sample Set Annotation Tool: Systemic inflammation is associated with differential gene expression and airway neutrophilia in asthma - GSE43397 [Systemic inflammation (SI), Asthma]

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Systemic inflammation is reported to be associated with neutrophilic airway inflammation in asthma, this study aimed to examine the molecular mechanisms of the neutrophilia that is associated with systemic inflammation, and hypothesized that asthma patients with systemic inflammation have a group of genes that are differentially expressed and are assciated with airway inflammation.

Hypothesis

Experimental Design

50 asthma patients were recruited and grouped as asthmatics with systemic inflammation (n=18) and asthamtics without systemic inflammation (n=16) accroding to the levels of serum CRP and IL-6. RNA was extracted from induced sputum and was reverse-transcribed into cDNA. Gene profiling was performed using Illumina Sentrix HumanRef-8 Version 2 Expression BeadChips, and genes that were differentially expressed between asthmatics with systemic inflammation and asthmatics without systemic inflammation were compared and valided using qPCR.

Experimental Variables

Systemic inflammation (defined in the dataset-associated publication as high CRP and IL-6 plasma levels) (2021 ICD-10-CM code* = Not Applicable)

Controls

Methods

Sample and gene profiling results were included in the analysis if the sample was of suitable purity (OD 260/280 ratio between 1.7-2.1) and was successfully amplified (sufficient cRNA generated) and hybridized (95th percentile of fluorescence score>500) and the data passed quality control criteria in GeneSpring GX (correlation coefficients and priciple component analysis plots)

Additional Information

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43397

Expected Samples:

50 Samples Loaded: 50

Species

Human (Homo sapiens)

Sample Source

Induced sputum

Disease

Systemic inflammation (defined in the dataset-associated publication as high CRP and IL-6 plasma levels)

Treatment Protocol

Growth Protocol

Extraction Protocol

RNA was extracted from induced sputum using the RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA quatitation was performed using the Quanti-iT RiboGreen RNA Quantitation Assay Kit (Molecular Probes Inc, Invitrogen, Eugene, OR, USA).

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	Gender	Grouping	sample_type	bmi	Sample title
SAMPLE 1	Male	SI Neg	induced sputum	26.2	4135447160_F
SAMPLE 10	Male	SI Neg	induced sputum	29.8	4135447194_D
SAMPLE 11	Male	SI Pos	induced sputum	29.7	4135447178_F
SAMPLE 12	Female	None	induced sputum	32.7	4310479173_C
SAMPLE 13	Male	SI Pos	induced sputum	42.8	4310479173_D

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File
GSE43397_Sample_Grouping.csv Sample Set Spreadsheet

Samples Viewer / Editor

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Sample ID	Gender	Grouping	Sample Type	Bmi	Sample title	Sample geo accession	Systemic inflammation group
SAMPLE 1	Male	SI Neg	induced sputum	26.2	4135447160_F	GSM1061931	SI(-)
SAMPLE 2	Male	None	induced sputum	17.3	4147931008_A	GSM1061932	None
SAMPLE 3	Female	SI Neg	induced sputum	21.38	4147931008_H	GSM1061933	SI(-)
SAMPLE 4	Female	SI Pos	induced sputum	40.63	4135447179_C	GSM1061934	SI(+)
SAMPLE 5	Female	SI Neg	induced sputum	25.83	4135447179_E	GSM1061935	SI(-)
SAMPLE 6	Female	SI Pos	induced sputum	28.7	4147931034_A	GSM1061936	SI(+)
SAMPLE 7	Male	SI Neg	induced sputum	34	4147931034_C	GSM1061937	SI(-)
SAMPLE 8	Female	None	induced sputum	22.6	4147931034_E	GSM1061938	10
SAMPLE 9	Female	SI Neg	induced sputum	24.3	4147931034_G	GSM1061939	SI(-)
SAMPLE 10	Male	SI Neg	induced sputum	29.8	4135447194_D	GSM1061940	SI(-)
SAMPLE 11	Male	SI Pos	induced sputum	29.7	4135447178_F	GSM1061941	SI(+)
SAMPLE 12	Female	None	induced sputum	32.7	4310479173_C	GSM1061942	None
SAMPLE 13	Male	SI Pos	induced sputum	42.8	4310479173_D	GSM1061943	SI(+)
SAMPLE 14	Female	None	induced sputum	25.3	4310479173_F	GSM1061944	15
SAMPLE 15	Female	SI Neg	induced sputum	24.9	4310479168_D	GSM1061945	SI(-)
SAMPLE 16	Female	None	induced sputum	22.8	4310479167_D	GSM1061946	None
SAMPLE 17	Female	SI Pos	induced sputum	33.9	4147931008_E	GSM1061947	SI(+)
SAMPLE 18	Female	SI Pos	induced sputum	38.9	4147931029_B	GSM1061948	SI(+)
SAMPLE 19	Male	SI Pos	induced sputum	36.1	4147931029_H	GSM1061949	SI(+)
SAMPLE 20	Female	SI Neg	induced sputum	24.2	4135447179_A	GSM1061950	SI(-)
SAMPLE 21	Male	SI Pos	induced sputum	33.8	4147931034_D	GSM1061951	SI(+)
SAMPLE 22	Female	None	induced sputum	29.8	4135447194_H	GSM1061952	3.5
SAMPLE 23	Male	SI Neg	induced sputum	25.5	4310479156_F	GSM1061953	SI(-)
SAMPLE 24	Male	SI Pos	induced sputum	40.9	4135447160_A	GSM1061954	SI(+)
SAMPLE 25	Female	SI Pos	induced sputum	42.7	4135447160_H	GSM1061955	SI(+)
SAMPLE 26	Male	None	induced sputum	28.3	4147931008_B	GSM1061956	24
SAMPLE 27	Male	SI Neg	induced sputum	30.2	4147931008_C	GSM1061957	SI(-)
SAMPLE 28	Female	None	induced sputum	38.1	4147931029_A	GSM1061958	None
SAMPLE 29	Female	None	induced sputum	34.5	4147931029_C	GSM1061959	0.2
SAMPLE 30	Male	SI Neg	induced sputum	29.66	4147931029_D	GSM1061960	SI(-)
SAMPLE 31	Female	SI Pos	induced sputum	35.9	4135447179_B	GSM1061961	SI(+)
SAMPLE 32	Female	SI Neg	induced sputum	22.4	4135447179_D	GSM1061962	SI(-)
SAMPLE 33	Male	SI Neg	induced sputum	30.3	4135447179_H	GSM1061963	SI(-)
SAMPLE 34	Female	SI Neg	induced sputum	29.8	4135447194_G	GSM1061964	SI(-)
SAMPLE 35	Female	SI Neg	induced sputum	21.5	4135447178_A	GSM1061965	SI(-)
SAMPLE 36	Female	None	induced sputum	29	4310479156_E	GSM1061966	None
SAMPLE 37	Male	None	induced sputum	37.7	4310479156_G	GSM1061967	25
SAMPLE 38	Male	None	induced sputum	27.7	4310479163_B	GSM1061968	None
SAMPLE 39	Female	SI Pos	induced sputum	22.1	4310479166_A	GSM1061969	SI(+)
SAMPLE 40	Female	SI Pos	induced sputum	40.8	4310479166_E	GSM1061970	SI(+)
SAMPLE 41	Female	SI Pos	induced sputum	58.9	4310479168_H	GSM1061971	SI(+)
SAMPLE 42	Female	SI Neg	induced sputum	22.2	4135447160_B	GSM1061972	SI(-)
SAMPLE 43	Male	None	induced sputum	26.9	4135447160_C	GSM1061973	50
SAMPLE 44	Female	None	induced sputum	34.3	4135447160_D	GSM1061974	6
SAMPLE 45	Male	None	induced sputum	30.4	4147931029_F	GSM1061975	30
SAMPLE 46	Female	SI Pos	induced sputum	44.7	4135447179_F	GSM1061976	SI(+)
SAMPLE 47	Male	SI Pos	induced sputum	29.2	4147931034_H	GSM1061977	SI(+)
SAMPLE 48	Female	SI Pos	induced sputum	33.7	4310479156_C	GSM1061978	SI(+)
SAMPLE 49	Female	SI Pos	induced sputum	26.9	4310479173_A	GSM1061979	SI(+)
SAMPLE 50	Male	None	induced sputum	27.7	4310479163_F	GSM1061980	30

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SIDRA