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Sample GSM1294252 Query DataSets for GSM1294252
Status Public on Sep 25, 2014
Title Cord_blood_Tartu_11
Sample type RNA
 
Source name Cord blood
Organism Homo sapiens
Characteristics country: Estonia
sample month: February
gender: Male
hla risk category (np=neutral/protective, m=medium, h=high, vh=very high): NP
dr3-dq2: -
dr4-dq8: -
gestational week: 40
hybridization batch: 1
Growth protocol Umbilical cord blood was drawn into Tempus Blood RNA tubes according to the manufacturer´s protocol and then stored in −70 °C until analyzed.
Extracted molecule total RNA
Extraction protocol Total whole-blood RNA was extracted from the samples using Tempus Spin RNA isolation kit (Applied Biosystems) according to manufacturer's instructions. RNA quality and quantity was determined using NanoDrop ND-2000 (Thermo Scientific) and Experion Automated Electrophoresis System (Bio-Rad Laboratories).
Label biotin
Label protocol 50 ng of total RNA was processed to cDNA with Ovation RNA amplification system v2, including the Ovation whole blood reagent (NuGEN Technologies). The amplified cDNA was subsequently biotin-labelled and fragmented with Encore biotin module (NuGEN Technologies).
 
Hybridization protocol Samples were hybridized to GeneChip Human Genome U219 array plate (Affymetrix) with manufacturer´s protocols for using the GeneTitan Hybridization, Wash and Stain Kit for 3’ IVT Array Plates (Affymetrix). GeneTitan MC Instrument (Affymetrix) was used to hybridize, wash, stain, and scan the arrays.
Scan protocol GeneTitan MC Instrument was used to scan the arrays. The probe cell intensity data was summarized with Affymetrix GeneChip Command Consol 3.1.
Data processing The intensity data was pre-processed using robust multi-array averaging (RMA). The absent call filtering was done by determining a threshold value empirically for each sample by fitting a two-component GMM for all non-control probesets. A probeset was filtered out if it was absent in at least 50 % of the samples from Espoo, Tartu and Petrozavodsk. Batch correction was done by applying the ComBat analysis method. Additional 15 rehybridized samples (in a separate data set) were utilized in this correction but excluded from further analysis steps. These intensities were then used to detect differential expression by fitting a linear model and computing a moderated t-statistic for each present probeset for all three contrasts: Espoo vs. Petrozavodsk, Tartu vs. Petrozavodsk and Espoo vs. Tartu. Gender, pregnancy week, month of birth and HLA risk class were included as confounding factors in the model.
 
Submission date Dec 18, 2013
Last update date Sep 26, 2014
Contact name Essi Laajala
E-mail(s) essi.laajala@btk.fi
Organization name Turku Centre for Biotechnology
Street address Tykistökatu 6
City Turku
ZIP/Postal code 20520
Country Finland
 
Platform ID GPL13667
Series (2)
GSE53471 Standard of hygiene and immune adaptation in newborn infants [113 cord blood RNA samples]
GSE53473 Standard of hygiene and immune adaptation in newborn infants

Data table header descriptions
ID_REF
VALUE Normalized and batch corrected log2 expression values

Data table
ID_REF VALUE
11715113_x_at 4.23275882320851
11715114_x_at 4.62663769960693
11715122_at 4.74744536164864
11715124_s_at 5.13275427127529
11715125_at 5.3561084599425
11715129_s_at 7.85781581802531
11715132_x_at 5.16667665120844
11715135_s_at 6.78071366212056
11715146_x_at 4.8877714538547
11715154_s_at 4.66133000536329
11715156_s_at 4.13069400367406
11715159_at 8.97021026122115
11715164_s_at 4.55239928044631
11715169_at 5.11588602711551
11715171_at 9.38606614221207
11715174_s_at 5.20205233496759
11715175_x_at 4.753328859202
11715177_s_at 5.02680749009332
11715178_s_at 4.29307614535366
11715181_x_at 4.9479426836097

Total number of rows: 26977

Table truncated, full table size 804 Kbytes.




Supplementary file Size Download File type/resource
GSM1294252_Tartu_11.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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