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Series GSE143153 Query DataSets for GSE143153
Status Public on Jul 24, 2020
Title Microarray analysis of salivary gland CD4+ T cells
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Whole human genome arrays were used to assess the transcriptome differences in CD3+CD4+CD45RA- memory T cells isolated and sorted from minor salivary gland biopsy tissue of individuals who met 2002 American European Consensus Group classification criteria for primary Sjogren’s syndrome (SS) and subjects who did not meet criteria for SS, lacked focal lymphocytic sialoadenitis, lacked anti-Ro antibodies, lacked anti-La antibodies, but who had subjective symptoms of dryness (non-SS, sicca controls).
Overall design Samples from 17 pSS and 15 non-SS subjects were hybridized to Agilent Whole Human Genome 8x60K microarrays in three batches (Batch 1: 2 pSS, 3 non-SS; Batch 2: 6 pSS, 5 non-SS; Batch 3: 9 pSS, 7 non-SS).  All data were pooled to assess potential batch effects by principal components analysis and gene expression data were quality control checked using the arrayQualityMetrics R package. Batch effects were equalized via ComBat analysis (‘Surrogate Variable Analysis’ R package Ver 3.8.0; manual specification of batches).
Contributor(s) Farris AD
Citation(s) 32650575
Submission date Jan 06, 2020
Last update date Aug 24, 2020
Contact name A. Darise Farris
Phone 405-271-7389
Organization name Oklahoma Medical Research Foundation
Department Arthritis & Clinical Immunology
Street address 825 NE 13th Street, MS 24
City Oklahoma City
State/province OK
ZIP/Postal code 73104
Country USA
Platforms (1)
GPL13607 Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (Feature Number version)
Samples (32)
GSM4251021 Subject 1_Primary SS_Batch 1
GSM4251022 Subject 2_Primary SS_Batch 1
GSM4251023 Subject 3_non-SS_Batch 1
BioProject PRJNA599110

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE143153_Processed_data_matrix.xlsx 31.4 Mb (ftp)(http) XLSX
GSE143153_RAW.tar 397.1 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
Processed data are available on Series record

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