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Sample GSM6321399 Query DataSets for GSM6321399
Status Public on Jun 07, 2023
Title CD4_SLE_P4_M
Sample type genomic
 
Source name CD4 DNA
Organism Homo sapiens
Characteristics cell type: CD4+ T cell
disease: SLE
Sex: Male
age: 78
ancestry: European-American
sledai score: 4
Extracted molecule genomic DNA
Extraction protocol Whole blood was collected from each previously recruited patient during clinic visits in vials containing EDTA. Peripheral blood mononuclear fractions were isolated using density centrifugation with Ficoll/Paque (GE Healthcare Life Sciences, Piscataway, NJ, USA). CD4+ T cell were isolated using MACS magnetic bead CD4+ T-cell isolation kit (Miltenyi Biosystems, Auburn, CA). Genomic DNA was isolated from the CD4+ T cells using Qiagen DNEasy kit (Qiagen, Germantown, MD, USA). 250ng of DNA from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo, Irvine, CA, USA) following the manufacturer’s instructions.
Label Cy5 and Cy3
Label protocol Standard protocol
 
Hybridization protocol Standard protocol
Scan protocol Standard protocol
Description Patient 4 (Male)
Data processing DNA methylation data analysis was performed in the R statistical computing environment (v.3.6.3). Raw .idat files were generated for each sample and underwent quality control and downstream analysis in the R package minfi (v.1.32.0). The following probes were removed based on best practices as used in DNAmArraypackage (v.0.1.1): probes with less than three beads and zero intensity values across all samples. Thereafter, correction for background signal and dye bias and normalization of signal intensities using functional normalization in the preprocessFunnorm.DNAmArray function was done. The first three principal component values, calculated from signal intensities of control probes present on all array spots to correct for technical variation, were utilized. More probes were removed, which included the following: probes with detection P-values < 0.01 and probes that returned signal intensities in fewer than 98% of samples. Remaining probes’ signal intensities were converted to M-values with limits of ±16. To reduce the number of probes with potential technical issues, we followed the criteria described by Zhou, Laird & Shen (2017) to mask any probes: a unique probe sequence of less than 30bp, mapping to multiple sites in the genome, polymorphisms that cause a color channel switching in type I probes, inconsistencies in specified reporter color channel and extension base, mapping to the Y chromosome, and/or having a polymorphism within 5bp of the 3’ end of the probe with a minor allele frequency (MAF) > 1% with exception of CpG-SNPs with C>T polymorphisms which we retained for analysis. ComBatfunction in the sva (v.3.34.0) package was used to perform batch correction.
Average Beta
 
Submission date Jul 10, 2022
Last update date Jun 07, 2023
Contact name Amr H Sawalha
E-mail(s) asawalha@pitt.edu
Organization name University of Pittsburgh
Street address 4401 Penn Avenue
City Pittsburgh
State/province PA
ZIP/Postal code 15224
Country USA
 
Platform ID GPL21145
Series (1)
GSE207861 Sex-based comparison of CD4+ T cell DNA methylation patterns in SLE reveals pro-inflammatory epigenetic changes in men

Data table header descriptions
ID_REF
VALUE M-values of each patient for each probe

Data table
ID_REF VALUE
cg18478105 -6.045660659
cg09835024 -3.197971781
cg14361672 3.144925814
cg01763666 -0.659654767
cg12950382 2.024273775
cg02115394 -2.740041848
cg25813447 -2.14971634
cg07779434 -5.018546127
cg13417420 -5.710027409
cg12480843 -5.150045088
cg26724186 3.860802671
cg24133276 -5.436579802
cg00617867 4.265329718
cg13773083 -0.766962094
cg17236668 4.324814073
cg19607165 -3.184791081
cg11073926 -4.514654393
cg08770523 -5.093675592
cg24652288 2.634456625
cg15998406 -2.474388005

Total number of rows: 847856

Table truncated, full table size 17052 Kbytes.




Supplementary file Size Download File type/resource
GSM6321399_205605870170_R02C01_Grn.idat.gz 7.0 Mb (ftp)(http) IDAT
GSM6321399_205605870170_R02C01_Red.idat.gz 7.1 Mb (ftp)(http) IDAT
Processed data included within Sample table
Processed data are available on Series record

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