Sample Set Annotation Tool: Whole blood mRNA expression profiling of host molecular networks in neonatal sepsis - GSE25504 - GPL6947

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

We aimed to identify the gene network and pathway biology associated with neonatal sepsis by determining genome-wide alterations in host RNA in infected infants

Hypothesis

Experimental Design

Samples were obtained from control and infected human neonates.

Experimental Variables

Sepsis (2021 ICD-10-CM code* = A41)

Controls

Methods

Raw scan data were background subtracted, VST transformed and subsequently robust spline normalised as performed by the lumi package of Bioconductor. Array probe features that had a present count in one or more samples were retained.

Additional Information

Expected Samples:

63 Samples Loaded: 63

Species

Human (Homo sapiens)

Sample Source

Whole Blood

Disease

Sepsis

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	!Sample Title	Gender	tissue	Grouping	neonate
GSM627008	Con001	Male	peripheral blood	control	control
GSM627009	Con017	Male	peripheral blood	control	control
GSM627010	Con021	Female	peripheral blood	control	control
GSM627011	Con022	Female	peripheral blood	control	control
GSM627012	Con028	Female	peripheral blood	control	control

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File
GSE25504 GPL6947 modified.csv Sample Set Spreadsheet
sampleset4000104_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	!Sample Title	Gender	Tissue	Grouping	Neonate	Birthweight (g)	Bloodculture result	Corrected gestational age (weeks+days)	On antibiotics at time of sample	Other positive results
GSM627008	Con001	Male	peripheral blood	control	control	1715	na	34+6	No	No
GSM627009	Con017	Male	peripheral blood	control	control	3250	na	40+6	No	No
GSM627010	Con021	Female	peripheral blood	control	control	3440	na	40+5	No	No
GSM627011	Con022	Female	peripheral blood	control	control	2990	na	41+6	No	No
GSM627012	Con028	Female	peripheral blood	control	control	2370	na	36+5	No	No
GSM627013	Con029	Male	peripheral blood	control	control	2940	na	39+6	No	No
GSM627014	Con040	Male	peripheral blood	control	control	2800	na	40+0	No	No
GSM627015	Con042	Male	peripheral blood	control	control	3980	na	42+5	No	umbilical swab grew anaerobes, coliforms, Saureus and gp B strep
GSM627016	Con043	Male	peripheral blood	control	control	3980	na	42+5	No	No
GSM627017	Con046	Female	peripheral blood	control	control	3500	na	41+6	No	No
GSM627018	Con048	Male	peripheral blood	control	control	4590	na	39+6	No	No
GSM627019	Con049	Female	peripheral blood	control	control	4140	na	41+5	No	No
GSM627020	Con051	Male	peripheral blood	control	control	3020	na	39+5	No	No
GSM627021	Con058	Male	peripheral blood	control	control	4120	na	39+5	No	No
GSM627022	Con062	Female	peripheral blood	control	control	4270	na	41+6	No	no. blood culture 3 days previously negative
GSM627023	Con063	Male	peripheral blood	control	control	3309	na	44+1	No	No
GSM627024	Con065	Female	peripheral blood	control	control	3620	na	42+1	No	No
GSM627025	Con067	Male	peripheral blood	control	control	2225	na	39+4	No	No
GSM627026	Con069	Male	peripheral blood	control	control	3510	na	40+2	No	No
GSM627027	Con071	Male	peripheral blood	control	control	4300	na	42+6	No	No
GSM627028	Con072	Male	peripheral blood	control	control	4370	na	41+0	No	No
GSM627029	Con073	Male	peripheral blood	control	control	1880	na	37+0	No	well. 3 days later had Saureus in wound swab.
GSM627030	Con077	Female	peripheral blood	control	control	3630	na	41+6	No	No
GSM627031	Con079	Female	peripheral blood	control	control	3440	na	40+1	No	No
GSM627032	Con081	Female	peripheral blood	control	control	3500	na	41+4	No	No
GSM627033	Con086	Male	peripheral blood	control	control	3820	na	43+1	No	No
GSM627034	Con087	Female	peripheral blood	control	control	2200	na	34+2	No	No
GSM627035	Con096	Male	peripheral blood	control	control	3700	na	37+5	No	No
GSM627036	Con097	Male	peripheral blood	control	control	4301	na	42+6	No	No
GSM627037	Con165	Female	peripheral blood	control	control	930	na	30+3	No	No
GSM627038	Con181	Female	peripheral blood	control	control	670	na	33+6	No	No
GSM627039	Con200	Male	peripheral blood	control	control	1115	na	35+2	No	No
GSM627040	Con202	Male	peripheral blood	control	control	1600	na	35+5	No	No
GSM627041	Con206	Male	peripheral blood	control	control	1225	na	32+3	No	No
GSM627042	Con207	Male	peripheral blood	control	control	4200	na	42+0	No	No
GSM627043	Inf009	Female	peripheral blood	infected	infected	720	Coagulase negative staphylococcus	32+5	Yes	coag neg staph long line tip next day, previous ureaplasma,,no previous positive blood cultures
GSM627044	Inf047	Male	peripheral blood	infected	infected	1380	candida	30+5	Yes	klebsiella in peritoneal fluid and ET secretions, NEC 1 week previously, candida in blood 4 days previously
GSM627045	Inf075	Female	peripheral blood	infected	infected	890	negative	36+4	No	CMV in blood and urine
GSM627046	Inf082	Male	peripheral blood	infected	infected	1230	positive (enterobacter cloacae)	30+1	Yes	enterobacter cloacae (also 1 week post sample)
GSM627047	Inf083	Female	peripheral blood	infected	infected	1405	Positive (E faecium)	34+1	Yes	Blood cultures 3 days before and 2 days after also E faecium
GSM627048	Inf084	Male	peripheral blood	infected	infected	720	Positive (coag neg staph)	29+3	Yes	CSF coag neg staph. Also from day before long line tip and BC grew coag neg staph
GSM627049	Inf089	Male	peripheral blood	infected	infected	850	positive (coag neg staph)	28+2	No	CSF and urine negative
GSM627050	Inf091	Female	peripheral blood	infected	infected	3900	Positive (Group B Strep)	38+1	No	CSF negative
GSM627051	Inf102	Female	peripheral blood	infected	infected	785	Positive (pseudomonas aeuruginosa and coag neg staph)	31+3	Yes	Blood culture positive for pseudomonas and coag neg staph, coag neg staph also present in blood cultures x 2 in previous week and also the next day
GSM627052	Inf111	Male	peripheral blood	infected	infected	1200	Coagulase negative staphylococcus	30+0	Yes	2 blood cultures coag neg staph
GSM627053	Inf112	Female	peripheral blood	infected	infected	660	Positive(group B strep)	25+3	No	CSF coag neg staph
GSM627054	Inf114	Female	peripheral blood	infected	infected	955	Positive(coag neg staph)	27+2	No	long line tip coag neg staph, previous day ETT tip and ETS Ecoli/coliforms
GSM627055	Inf116	Male	peripheral blood	infected	infected	720	negative	30+0	Yes	aspirate of abscess grew coag neg staph
GSM627056	Inf119	Female	peripheral blood	infected	infected	983	Coagulase negative staphylococcus	30+2	Yes	No
GSM627057	Inf125	Female	peripheral blood	infected	infected	983	Postive (coag neg staph)	29+5	Yes	blood culture 5 days previous grew coag neg staph
GSM627058	Inf132	Male	peripheral blood	infected	infected	1100	Positive (E faecalis)	29+2	Yes	blood culture 2 and 4 days previously and next day also enterococcus
GSM627059	Inf133	Male	peripheral blood	infected	infected	1140	Coagulase negative staphylococcus	27+4	Yes	No
GSM627060	Inf138	Female	peripheral blood	infected	infected	870	Positive (coag neg staph)	27+2	Yes	No
GSM627061	Inf145	Male	peripheral blood	infected	infected	1100	Enterococcus faecalis	28+5	Yes	No
GSM627062	Inf149	Female	peripheral blood	infected	infected	840	negative	29+1	Yes	1cfu Klebsiells in CSF
GSM627063	Inf152	Male	peripheral blood	infected	infected	450	positive(coag neg staph)	31+0	Yes	blood culture 3 days previous 2 strains coag neg staph, line tip 2 days previous mixed coag neg staph
GSM627064	Inf157	Female	peripheral blood	infected	infected	820	Coagulase negative staphylococcus	31+3	No	No
GSM627065	Inf159	Male	peripheral blood	infected	infected	1335	positive(enterococcus)	31+2	No	csf 1 no growth, 2 coag neg staph
GSM627066	Inf162	Male	peripheral blood	infected	infected	1130	positive(coag neg staph)	27+6	No	2 separate blood cultures coag neg staph, csf no growth
GSM627067	Inf164	Female	peripheral blood	infected	infected	820	positive(kelbsiella oxytoca)	31+5	Yes	not stated
GSM627068	Inf191	Male	peripheral blood	infected	infected	2970	positive(E coli)	37+0	No	csf no growth
GSM627069	Inf198	Male	peripheral blood	infected	infected	1070	positive(coag neg staph)	33+1	No	csf no growth, note CoNeg Staph resistant to fluclox and gent which baby on further deterioration and repeat sample though…
GSM627070	Inf203	Male	peripheral blood	infected	infected	1070	Coagulase negative staphylococcus	37+0	No	No

Group Sets View in Gene Expression Browser

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Module Analysis

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