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

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

Controls

Methods

Additional Information

Expected Samples:

63 Samples Loaded: 63

Species

Human (Homo sapiens)

Sample Source

Whole Blood , Neonatal

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	neonate	Bloodculture result
GSM627008	Con001	Male	peripheral blood	control	na
GSM627009	Con017	Male	peripheral blood	control	na
GSM627010	Con021	Female	peripheral blood	control	na
GSM627011	Con022	Female	peripheral blood	control	na
GSM627012	Con028	Female	peripheral blood	control	na

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File

GSE25504 GPL6947 modified.csv Sample Set Spreadsheet

Samples Viewer / Editor

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

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