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Clinical

This SuperSeries is composed of the following SubSeries: GSE53471, Standard of hygiene and immune adaptation in newborn infants [113 cord blood RNA samples]; and GSE53472, Standard of hygiene and immune adaptation in newborn infants [15 rehybridized/batch correction samples].

Purpose

The prevalence of immune-mediated diseases such as allergies and autoimmune diseases is on the rise in the developed world. Microbial exposure is known to modulate the risk for these diseases. In order to explore differences in the gene expression patterns induced in utero in infants born in contrasting standards of living and hygiene, we collected umbilical cord blood RNA samples from full-term newborn infants born with normal vaginal delivery in Finland (modern society), Estonia (rapidly developing society) and the Republic of Karelia, Russia (poor economical conditions). Transcriptomic profiles were analyzed using whole genome microarrays including gender, gestational age, birth month and HLA allele genotype as confounding variables in the analysis. The data revealed that the whole blood transcriptome of Finnish and Estonian neonates differ from their Karelian counterparts. Samples from Karelian infants had an increase in transcripts associated with LPS induction and bacterial sepsis observed in 1-year-old infants in earlier studies. The results suggest exposure to toll like receptor (TLR) ligands and a more matured immune response in infants born in Petrozavodsk compared to the Finnish and Estonian infants. These results further support the concept of a conspicuous plasticity in the developing immune system: the environmental factors that play a role in the susceptibility/protection towards immune-mediated diseases begin to shape the neonatal immunity already in utero and direct the maturation of both the adaptive and the innate immune responses in accordance with the surrounding microbial milieu.

Hypothesis

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Experimental Design

Umbilical cord blood was drawn into Tempus Blood RNA tubes (Applied Biosystems) from children born between January and May 2010 at the maternity unit of Jorvi hospital (Espoo, Finland; n=48), maternity units of Tartu and Põlva (Estonia; n=25), or two maternity departments in Petrozavodsk (capital of the Republic of Karelia, Russian Federation; n=40) according to the manufacturer´s protocol and then stored in ?70 °C until analyzed. All newborn infants were full-term (>36 gestational weeks) and born vaginally. 113 cord blood RNA samples were analyzed with Affymetrix U219 gene array. Gender, pregnancy week, month of birth and HLA risk class were included as confounding factors in the analysis model.

Experimental Variables

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Controls

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Methods

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Additional Information

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Microarray
Affymetrix HG-U219 v1
128 Samples Loaded: 128
Human (Homo sapiens)
Whole Blood , Neonatal
Sample Set Spreadsheet
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Samples Preview
Sample ID !Sample Title Gender dr4-dq8 dr3-dq2 country
GSM1294154 Cord_blood_Espoo_1 Male - - Finland
GSM1294155 Cord_blood_Espoo_2 Female - + Finland
GSM1294156 Cord_blood_Espoo_3 Male - + Finland
GSM1294157 Cord_blood_Espoo_4 Female + - Finland
GSM1294158 Cord_blood_Espoo_5 Male - - Finland
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Sample ID !Sample Title Gender Dr4-dq8 Dr3-dq2 Country Hla risk category (np=neutral/protective, m=medium, h=high, vh=very high) Hybridization batch Sample month Gestational week Group name
GSM1294154
Cord_blood_Espoo_1
Male
-
-
Finland
NP
2
April
42
Espoo
GSM1294155
Cord_blood_Espoo_2
Female
-
+
Finland
M
2
April
39
Espoo
GSM1294156
Cord_blood_Espoo_3
Male
-
+
Finland
M
2
April
38
Espoo
GSM1294157
Cord_blood_Espoo_4
Female
+
-
Finland
NP
2
April
40
Espoo
GSM1294158
Cord_blood_Espoo_5
Male
-
-
Finland
NP
1
March
42
Espoo
GSM1294159
Cord_blood_Espoo_6
Male
-
-
Finland
NP
1
April
40
Espoo
GSM1294160
Cord_blood_Espoo_7
Female
-
-
Finland
NP
1
April
39
Espoo
GSM1294161
Cord_blood_Espoo_8
Male
-
-
Finland
NP
1
January
40
Espoo
GSM1294162
Cord_blood_Espoo_9
Male
+
-
Finland
NP
1
January
41
Espoo
GSM1294163
Cord_blood_Espoo_10
Male
+
-
Finland
H
1
January
42
Espoo
GSM1294164
Cord_blood_Espoo_11
Female
-
-
Finland
NP
1
January
39
Espoo
GSM1294165
Cord_blood_Espoo_12
Male
-
-
Finland
NP
1
January
39
Espoo
GSM1294166
Cord_blood_Espoo_13
Female
-
-
Finland
NP
4
January
42
Espoo
GSM1294167
Cord_blood_Espoo_14
Male
+
-
Finland
H
1
January
38
Espoo
GSM1294168
Cord_blood_Espoo_15
Male
-
-
Finland
NP
1
January
40
Espoo
GSM1294169
Cord_blood_Espoo_16
Male
-
-
Finland
NP
1
January
42
Espoo
GSM1294170
Cord_blood_Espoo_17
Female
-
+
Finland
NP
1
January
41
Espoo
GSM1294171
Cord_blood_Espoo_18
Female
-
-
Finland
NP
1
February
40
Espoo
GSM1294172
Cord_blood_Espoo_19
Male
-
-
Finland
NP
1
February
39
Espoo
GSM1294173
Cord_blood_Espoo_20
Female
-
-
Finland
NP
1
February
41
Espoo
GSM1294174
Cord_blood_Espoo_21
Female
-
-
Finland
NP
1
February
37
Espoo
GSM1294175
Cord_blood_Espoo_22
Female
-
-
Finland
NP
1
February
41
Espoo
GSM1294176
Cord_blood_Espoo_23
Male
-
+
Finland
M
1
February
40
Espoo
GSM1294177
Cord_blood_Espoo_24
Male
+
-
Finland
H
1
February
40
Espoo
GSM1294178
Cord_blood_Espoo_25
Female
-
-
Finland
NP
1
February
39
Espoo
GSM1294179
Cord_blood_Espoo_26
Male
-
-
Finland
NP
1
February
38
Espoo
GSM1294180
Cord_blood_Espoo_27
Female
-
-
Finland
NP
1
February
41
Espoo
GSM1294181
Cord_blood_Espoo_28
Female
-
-
Finland
NP
1
February
39
Espoo
GSM1294182
Cord_blood_Espoo_29
Female
-
-
Finland
NP
4
February
41
Espoo
GSM1294183
Cord_blood_Espoo_30
Male
+
-
Finland
NP
1
February
38
Espoo
GSM1294184
Cord_blood_Espoo_31
Male
-
+
Finland
M
1
February
39
Espoo
GSM1294185
Cord_blood_Espoo_32
Male
+
-
Finland
NP
1
February
40
Espoo
GSM1294186
Cord_blood_Espoo_33
Female
-
-
Finland
NP
1
February
39
Espoo
GSM1294187
Cord_blood_Espoo_34
Male
-
-
Finland
NP
1
February
40
Espoo
GSM1294188
Cord_blood_Espoo_35
Female
+
-
Finland
H
1
February
41
Espoo
GSM1294189
Cord_blood_Espoo_36
Female
-
-
Finland
NP
1
February
41
Espoo
GSM1294190
Cord_blood_Espoo_37
Female
+
+
Finland
VH
4
February
39
Espoo
GSM1294191
Cord_blood_Espoo_38
Female
-
+
Finland
NP
1
February
42
Espoo
GSM1294192
Cord_blood_Espoo_39
Female
+
-
Finland
H
1
March
41
Espoo
GSM1294193
Cord_blood_Espoo_40
Male
-
-
Finland
NP
1
March
40
Espoo
GSM1294194
Cord_blood_Espoo_41
Female
-
-
Finland
NP
1
March
39
Espoo
GSM1294195
Cord_blood_Espoo_42
Male
-
-
Finland
NP
1
March
41
Espoo
GSM1294196
Cord_blood_Espoo_43
Male
-
-
Finland
NP
1
March
41
Espoo
GSM1294197
Cord_blood_Espoo_44
Male
+
-
Finland
H
4
March
41
Espoo
GSM1294198
Cord_blood_Espoo_45
Male
-
-
Finland
NP
1
March
38
Espoo
GSM1294199
Cord_blood_Espoo_46
Female
-
-
Finland
NP
1
March
40
Espoo
GSM1294200
Cord_blood_Espoo_47
Male
+
+
Finland
VH
1
April
37
Espoo
GSM1294201
Cord_blood_Espoo_48
Male
-
-
Finland
NP
1
April
38
Espoo
GSM1294202
Cord_blood_Petrozavodsk_1
Male
-
-
Russia
NP
3
January
40
Petrozavodsk
GSM1294203
Cord_blood_Petrozavodsk_2
Female
-
-
Russia
NP
3
January
41
Petrozavodsk
GSM1294204
Cord_blood_Petrozavodsk_3
Female
-
-
Russia
NP
3
February
40
Petrozavodsk
GSM1294205
Cord_blood_Petrozavodsk_4
Male
-
-
Russia
NP
3
February
39
Petrozavodsk
GSM1294206
Cord_blood_Petrozavodsk_5
Female
-
-
Russia
NP
4
February
40
Petrozavodsk
GSM1294207
Cord_blood_Petrozavodsk_6
Female
+
-
Russia
H
3
February
40
Petrozavodsk
GSM1294208
Cord_blood_Petrozavodsk_7
Male
+
-
Russia
NP
3
February
41
Petrozavodsk
GSM1294209
Cord_blood_Petrozavodsk_8
Male
-
-
Russia
NP
3
March
42
Petrozavodsk
GSM1294210
Cord_blood_Petrozavodsk_9
Female
-
-
Russia
NP
4
March
42
Petrozavodsk
GSM1294211
Cord_blood_Petrozavodsk_10
Male
-
-
Russia
NP
3
March
40
Petrozavodsk
GSM1294212
Cord_blood_Petrozavodsk_11
Female
-
-
Russia
NP
3
March
40
Petrozavodsk
GSM1294213
Cord_blood_Petrozavodsk_12
Male
-
-
Russia
NP
3
March
39
Petrozavodsk
GSM1294214
Cord_blood_Petrozavodsk_13
Female
-
-
Russia
NP
3
March
41
Petrozavodsk
GSM1294215
Cord_blood_Petrozavodsk_14
Female
-
+
Russia
M
3
March
40
Petrozavodsk
GSM1294216
Cord_blood_Petrozavodsk_15
Female
-
-
Russia
NP
4
March
40
Petrozavodsk
GSM1294217
Cord_blood_Petrozavodsk_16
Male
-
+
Russia
M
3
March
38
Petrozavodsk
GSM1294218
Cord_blood_Petrozavodsk_17
Male
+
-
Russia
NP
3
March
40
Petrozavodsk
GSM1294219
Cord_blood_Petrozavodsk_18
Female
-
-
Russia
NP
3
March
40
Petrozavodsk
GSM1294220
Cord_blood_Petrozavodsk_19
Male
-
-
Russia
NP
4
March
40
Petrozavodsk
GSM1294221
Cord_blood_Petrozavodsk_20
Male
-
-
Russia
NP
4
March
40
Petrozavodsk
GSM1294222
Cord_blood_Petrozavodsk_21
Male
+
-
Russia
H
3
March
37
Petrozavodsk
GSM1294223
Cord_blood_Petrozavodsk_22
Female
-
-
Russia
NP
3
March
40
Petrozavodsk
GSM1294224
Cord_blood_Petrozavodsk_23
Male
-
-
Russia
NP
3
March
40
Petrozavodsk
GSM1294225
Cord_blood_Petrozavodsk_24
Female
-
-
Russia
NP
3
March
40
Petrozavodsk
GSM1294226
Cord_blood_Petrozavodsk_25
Female
-
-
Russia
NP
3
March
37
Petrozavodsk
GSM1294227
Cord_blood_Petrozavodsk_26
Male
+
-
Russia
H
3
March
40
Petrozavodsk
GSM1294228
Cord_blood_Petrozavodsk_27
Male
-
-
Russia
NP
3
March
41
Petrozavodsk
GSM1294229
Cord_blood_Petrozavodsk_28
Male
-
-
Russia
NP
3
March
40
Petrozavodsk
GSM1294230
Cord_blood_Petrozavodsk_29
Female
+
-
Russia
NP
3
April
40
Petrozavodsk
GSM1294231
Cord_blood_Petrozavodsk_30
Male
-
-
Russia
NP
3
April
40
Petrozavodsk
GSM1294232
Cord_blood_Petrozavodsk_31
Male
-
-
Russia
NP
3
April
38
Petrozavodsk
GSM1294233
Cord_blood_Petrozavodsk_32
Male
-
-
Russia
NP
4
April
40
Petrozavodsk
GSM1294234
Cord_blood_Petrozavodsk_33
Male
-
+
Russia
NP
3
April
40
Petrozavodsk
GSM1294235
Cord_blood_Petrozavodsk_34
Male
+
-
Russia
H
3
April
40
Petrozavodsk
GSM1294236
Cord_blood_Petrozavodsk_35
Female
-
+
Russia
NP
3
May
40
Petrozavodsk
GSM1294237
Cord_blood_Petrozavodsk_36
Female
-
-
Russia
NP
3
May
40
Petrozavodsk
GSM1294238
Cord_blood_Petrozavodsk_37
Female
-
-
Russia
NP
3
May
40
Petrozavodsk
GSM1294239
Cord_blood_Petrozavodsk_38
Male
-
-
Russia
NP
3
May
39
Petrozavodsk
GSM1294240
Cord_blood_Petrozavodsk_39
Female
-
-
Russia
NP
3
May
40
Petrozavodsk
GSM1294241
Cord_blood_Petrozavodsk_40
Male
-
-
Russia
NP
4
May
38
Petrozavodsk
GSM1294242
Cord_blood_Tartu_1
Male
+
+
Estonia
VH
4
January
38
Tartu
GSM1294243
Cord_blood_Tartu_2
Female
-
-
Estonia
NP
1
January
40
Tartu
GSM1294244
Cord_blood_Tartu_3
Female
-
-
Estonia
NP
1
January
40
Tartu
GSM1294245
Cord_blood_Tartu_4
Male
-
-
Estonia
NP
1
February
38
Tartu
GSM1294246
Cord_blood_Tartu_5
Female
-
-
Estonia
NP
1
February
40
Tartu
GSM1294247
Cord_blood_Tartu_6
Male
-
-
Estonia
NP
1
February
37
Tartu
GSM1294248
Cord_blood_Tartu_7
Female
-
-
Estonia
NP
1
February
41
Tartu
GSM1294249
Cord_blood_Tartu_8
Male
+
-
Estonia
H
1
February
40
Tartu
GSM1294250
Cord_blood_Tartu_9
Female
-
+
Estonia
NP
1
February
42
Tartu
GSM1294251
Cord_blood_Tartu_10
Male
-
+
Estonia
NP
1
February
38
Tartu
GSM1294252
Cord_blood_Tartu_11
Male
-
-
Estonia
NP
1
February
40
Tartu
GSM1294253
Cord_blood_Tartu_12
Female
-
-
Estonia
NP
1
February
40
Tartu
GSM1294254
Cord_blood_Tartu_13
Female
-
+
Estonia
NP
1
February
41
Tartu
GSM1294255
Cord_blood_Tartu_14
Female
-
-
Estonia
NP
1
February
39
Tartu
GSM1294256
Cord_blood_Tartu_15
Female
-
-
Estonia
NP
1
February
39
Tartu
GSM1294257
Cord_blood_Tartu_16
Female
-
-
Estonia
NP
1
February
39
Tartu
GSM1294258
Cord_blood_Tartu_17
Male
-
-
Estonia
NP
4
February
41
Tartu
GSM1294259
Cord_blood_Tartu_18
Female
-
-
Estonia
NP
1
April
41
Tartu
GSM1294260
Cord_blood_Tartu_19
Female
-
-
Estonia
NP
1
April
42
Tartu
GSM1294261
Cord_blood_Tartu_20
Female
-
-
Estonia
NP
4
April
40
Tartu
GSM1294262
Cord_blood_Tartu_21
Male
-
-
Estonia
NP
1
April
37
Tartu
GSM1294263
Cord_blood_Tartu_22
Female
-
-
Estonia
NP
1
April
41
Tartu
GSM1294264
Cord_blood_Tartu_23
Female
-
-
Estonia
NP
1
May
40
Tartu
GSM1294265
Cord_blood_Tartu_24
Male
-
+
Estonia
M
4
May
40
Tartu
GSM1294266
Cord_blood_Tartu_25
Male
-
-
Estonia
NP
1
May
41
Tartu
GSM1294267
Cord_blood_Espoo_13_rehybridized
Female
-
-
Finland
NP
1
January
42
Tartu
GSM1294268
Cord_blood_Espoo_29_rehybridized
Female
-
-
Finland
NP
1
February
41
Tartu
GSM1294269
Cord_blood_Espoo_37_rehybridized
Female
+
+
Finland
VH
1
February
39
Tartu
GSM1294270
Cord_blood_Espoo_44_rehybridized
Male
+
-
Finland
H
1
March
41
Tartu
GSM1294271
Cord_blood_Petrozavodsk_5_rehybridized
Female
-
-
Russia
NP
3
February
40
Petrozavodsk
GSM1294272
Cord_blood_Petrozavodsk_9_rehybridized
Female
-
-
Russia
NP
3
March
42
Petrozavodsk
GSM1294273
Cord_blood_Petrozavodsk_15_rehybridized
Female
-
-
Russia
NP
3
March
40
Petrozavodsk
GSM1294274
Cord_blood_Petrozavodsk_19_rehybridized
Male
-
-
Russia
NP
3
March
40
Petrozavodsk
GSM1294275
Cord_blood_Petrozavodsk_20_rehybridized
Male
-
-
Russia
NP
3
March
40
Petrozavodsk
GSM1294276
Cord_blood_Petrozavodsk_32_rehybridized
Male
-
-
Russia
NP
3
April
40
Petrozavodsk
GSM1294277
Cord_blood_Petrozavodsk_40_rehybridized
Male
-
-
Russia
NP
3
May
38
Petrozavodsk
GSM1294278
Cord_blood_Tartu_1_rehybridized
Male
+
+
Estonia
VH
1
January
38
Tartu
GSM1294279
Cord_blood_Tartu_17_rehybridized
Male
-
-
Estonia
NP
1
February
41
Tartu
GSM1294280
Cord_blood_Tartu_20_rehybridized
Female
-
-
Estonia
NP
1
April
40
Tartu
GSM1294281
Cord_blood_Tartu_24_rehybridized
Male
-
+
Estonia
M
1
May
40
Tartu

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