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Clinical

Whole blood mRNA expression profiling of host molecular networks in neonatal sepsis. Subset of GSE25504 using platform GPL6947

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

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Experimental Design

Samples were obtained from control and infected human neonates.

Experimental Variables

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

Controls

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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

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Microarray
Illumina HumanHT-12 v3
63 Samples Loaded: 63
Human (Homo sapiens)
Whole Blood
Sepsis
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
Please log in in order to upload files.
File
GSE25504 GPL6947 modified.csv
Sample Set Spreadsheet
sampleset4000104_sampleannotations.csv
Sample Set Spreadsheet
Log2 Transformed
Raw Signal
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Clinical Datasource
Links

Samples Viewer / Editor

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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

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