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In Progress
Clinical

Dataset with samples from Individuals with:

A- Combined immunodeficiencies with associated or syndromic features:

1)- HOLI1/RBCK1 deficiency, Phenotype OMIM number 615895

PID classification: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4659841/

Purpose

HOIL-1 deficient disease is a new early onset fatal autosomal recessive human disorder charaterized by chronic auto-inflammation, recurrent invasive bacterial infections and progressive muscular amylopectinosis. We studied the effect of TNF-? and IL-1? on transcriptional changes of PBMCs from HOIL-1- and MYD88-deficient patients.

Hypothesis

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Experimental Design

PBMCs were obtained from HOIL-1 and MYD88-deficient patients and healthy donors and stimulated with TNF-? or IL-1? for 2 and 6 hours. RNA were extracted. Labeled cRNA were hybridized to Illumina Human HT-12 V4 Beadchips.

Experimental Variables

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Controls

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Methods

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Additional Information

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Microarray
Illumina HumanHT-12 v4
45 Samples Loaded: 45
Human (Homo sapiens)
PBMC
HOIL1 deficiency
Sample Set Spreadsheet
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Samples Preview
Sample ID !Sample Title group time subject Cell type
GSM1003013 PBMC C1 IL1 -2h 6334175045_G Control IL1b 2h 2 hours Healthy 1 PBMC
GSM1003014 PBMC C1 IL1 -6h 6334175036_L Control IL1b 6h 6 hours Healthy 1 PBMC
GSM1003015 PBMC C1 Non stimulate -2h 6334175027_F Control no stimulation 2h 2 hours Healthy 1 PBMC
GSM1003016 PBMC C1 Non stimulate -6h 6334175046_L Control no stimulation 6h 6 hours Healthy 1 PBMC
GSM1003017 PBMC C1 TNF -2h 6334175027_I Control TNFa 2h 2 hours Healthy 1 PBMC
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File
sampleset4000035_sampleannotations_Group.csv
Sample Set Spreadsheet
sampleset4000035_sampleannotations_Group.csv
Sample Set Spreadsheet
sampleset4000035_sampleannotations_Group.csv
Sample Set Spreadsheet
Raw Signal
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Sample ID !Sample Title Group Time Subject Cell type Stimulation Disease state
GSM1003013
PBMC C1 IL1 -2h 6334175045_G
Control IL1b 2h
2 hours
Healthy 1
PBMC
IL-1b
Healthy
GSM1003014
PBMC C1 IL1 -6h 6334175036_L
Control IL1b 6h
6 hours
Healthy 1
PBMC
IL-1b
Healthy
GSM1003015
PBMC C1 Non stimulate -2h 6334175027_F
Control no stimulation 2h
2 hours
Healthy 1
PBMC
Medium
Healthy
GSM1003016
PBMC C1 Non stimulate -6h 6334175046_L
Control no stimulation 6h
6 hours
Healthy 1
PBMC
Medium
Healthy
GSM1003017
PBMC C1 TNF -2h 6334175027_I
Control TNFa 2h
2 hours
Healthy 1
PBMC
TNF-a
Healthy
GSM1003018
PBMC C1 TNF -6h 6334175045_B
Control TNFa 6h
6 hours
Healthy 1
PBMC
TNF-a
Healthy
GSM1003019
PBMC C2 IL1 -2h 6334175027_A
Control IL1b 2h
2 hours
Healthy 2
PBMC
IL-1b
Healthy
GSM1003020
PBMC C2 IL1 -6h 6334175048_A
Control IL1b 6h
6 hours
Healthy 2
PBMC
IL-1b
Healthy
GSM1003021
PBMC C2 Non stimulate -2h 6334175044_H
Control no stimulation 2h
2 hours
Healthy 2
PBMC
Medium
Healthy
GSM1003022
PBMC C2 Non stimulate -6h 6334175044_A
Control no stimulation 6h
6 hours
Healthy 2
PBMC
Medium
Healthy
GSM1003023
PBMC C2 TNF -2h 6334175045_H
Control TNFa 2h
2 hours
Healthy 2
PBMC
TNF-a
Healthy
GSM1003024
PBMC C2 TNF -6h 6334175030_D
Control TNFa 6h
6 hours
Healthy 3
PBMC
TNF-a
Healthy
GSM1003025
PBMC C3 IL1 -2h 6334175048_B
Control IL1b 2h
2 hours
Healthy 3
PBMC
IL-1b
Healthy
GSM1003026
PBMC C3 IL1 -6h 6334175030_L
Control IL1b 6h
6 hours
Healthy 3
PBMC
IL-1b
Healthy
GSM1003027
PBMC C3 Non stimulate -2h 6334175027_L
Control no stimulation 2h
2 hours
Healthy 3
PBMC
Medium
Healthy
GSM1003028
PBMC C3 Non stimulate -6h 6334175040_J
Control no stimulation 6h
6 hours
Healthy 3
PBMC
Medium
Healthy
GSM1003029
PBMC C3 TNF -2h 6334175026_C
Control TNFa 2h
2 hours
Healthy 3
PBMC
TNF-a
Healthy
GSM1003030
PBMC C3 TNF -6h 6334175045_J
Control TNFa 6h
6 hours
Healthy 3
PBMC
TNF-a
Healthy
GSM1003031
PBMC MYD88-(1) IL1 -2h 6334175030_K
MYD88 IL1b 2h
2 hours
Myd88 deficiency 1
PBMC
IL-1b
Myd88 deficiency
GSM1003032
PBMC MYD88-(1) IL1 -6h 6334175029_B
MYD88 IL1b 6h
6 hours
Myd88 deficiency 1
PBMC
IL-1b
Myd88 deficiency
GSM1003033
PBMC MYD88-(1) Non stimulate -2h 6334175031_I
MYD88 no stimulation 2h
2 hours
Myd88 deficiency 1
PBMC
Medium
Myd88 deficiency
GSM1003034
PBMC MYD88-(1) Non stimulate -6h 6334175040_D
MYD88 no stimulation 6h
6 hours
Myd88 deficiency 1
PBMC
Medium
Myd88 deficiency
GSM1003035
PBMC MYD88-(1) TNF -2h 6334175036_B
MYD88 TNFa 2h
2 hours
Myd88 deficiency 1
PBMC
TNF-a
Myd88 deficiency
GSM1003036
PBMC MYD88-(1) TNF -6h 6334175048_C
MYD88 TNFa 6h
6 hours
Myd88 deficiency 1
PBMC
TNF-a
Myd88 deficiency
GSM1003037
PBMC MYD88-(2) IL1 -2h 6334175029_D
MYD88 IL1b 2h
2 hours
Myd88 deficiency 2
PBMC
IL-1b
Myd88 deficiency
GSM1003038
PBMC MYD88-(2) IL1 -6h 6334175036_K
MYD88 IL1b 6h
6 hours
Myd88 deficiency 2
PBMC
IL-1b
Myd88 deficiency
GSM1003039
PBMC MYD88-(2) Non stimulate -2h 6334175040_L
MYD88 no stimulation 2h
2 hours
Myd88 deficiency 2
PBMC
Medium
Myd88 deficiency
GSM1003040
PBMC MYD88-(2) Non stimulate -6h 6334175036_H
MYD88 no stimulation 6h
6 hours
Myd88 deficiency 2
PBMC
Medium
Myd88 deficiency
GSM1003041
PBMC MYD88-(2) TNF -2h 6334175030_H
MYD88 TNFa 2h
2 hours
Myd88 deficiency 2
PBMC
TNF-a
Myd88 deficiency
GSM1003042
PBMC MYD88-(2) TNF -6h 6334175036_A
MYD88 TNFa 6h
6 hours
Myd88 deficiency 2
PBMC
TNF-a
Myd88 deficiency
GSM1003043
PBMC P1 IL1 -6h 6334175029_E
HOIL IL1b 6h
6 hours
HOIL deficiency 1
PBMC
IL-1b
HOIL deficiency
GSM1003044
PBMC P1 Non stimulate -6h 6334175026_H
HOIL no stimulation 6h
6 hours
HOIL deficiency 1
PBMC
Medium
HOIL deficiency
GSM1003045
PBMC P1 TNF -6h 6334175036_C
HOIL TNFa 6h
6 hours
HOIL deficiency 1
PBMC
TNF-a
HOIL deficiency
GSM1003046
PBMC P2 IL1 -2h 6334175045_L
HOIL IL1b 2h
2 hours
HOIL deficiency 2
PBMC
IL-1b
HOIL deficiency
GSM1003047
PBMC P2 IL1 -6h 6334175027_E
HOIL IL1b 6h
6 hours
HOIL deficiency 2
PBMC
IL-1b
HOIL deficiency
GSM1003048
PBMC P2 Non stimulate -2h 6334175031_G
HOIL no stimulation 2h
2 hours
HOIL deficiency 2
PBMC
Medium
HOIL deficiency
GSM1003049
PBMC P2 Non stimulate -6h 6334175044_F
HOIL no stimulation 6h
6 hours
HOIL deficiency 2
PBMC
Medium
HOIL deficiency
GSM1003050
PBMC P2 TNF -2h 6334175046_I
HOIL TNFa 2h
2 hours
HOIL deficiency 2
PBMC
TNF-a
HOIL deficiency
GSM1003051
PBMC P2 TNF -6h 6334175036_G
HOIL TNFa 6h
6 hours
HOIL deficiency 2
PBMC
TNF-a
HOIL deficiency
GSM1003052
PBMC P3 IL1 -2h 6334175029_C
HOIL IL1b 2h
2 hours
HOIL deficiency 3
PBMC
IL-1b
HOIL deficiency
GSM1003053
PBMC P3 IL1 -6h 6334175026_J
HOIL IL1b 6h
6 hours
HOIL deficiency 3
PBMC
IL-1b
HOIL deficiency
GSM1003054
PBMC P3 Non stimulate -2h 6334175031_E
HOIL no stimulation 2h
2 hours
HOIL deficiency 3
PBMC
Medium
HOIL deficiency
GSM1003055
PBMC P3 Non stimulate -6h 6334175045_E
HOIL no stimulation 6h
6 hours
HOIL deficiency 3
PBMC
Medium
HOIL deficiency
GSM1003056
PBMC P3 TNF -2h 6334175036_J
HOIL TNFa 2h
2 hours
HOIL deficiency 3
PBMC
TNF-a
HOIL deficiency
GSM1003057
PBMC P3 TNF -6h 6334175045_C
HOIL TNFa 6h
6 hours
HOIL deficiency 3
PBMC
TNF-a
HOIL deficiency

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