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Clinical

The effect of cell subset isolation method on gene expression in leukocytes-GSE50008

Purpose

Analysis of the effect of isolation methods (fluorescence activated cell sorting (FACS), positive and negative immunomagnetic selection) on gene expression in human primary CD4+, CD8+ T cells, B cells and monocytes.FACS incurs the least short-term changes in gene expression signature.

Hypothesis

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Experimental Design

This study evaluated the short-term effects on gene expression in four leukocyte subsets (CD4+, CD8+ T cells, B cells and monocytes) of the three commonly used isolation methods (FACS, positive and negative selection) in order to identify the optimal method for cell isolation for gene expression studies in patient samples where gene expression pertaining to a disease state or treatment is of interest and gene expression caused by cell handing is minimized.

Experimental Variables

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Controls

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Methods

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Additional Information
  • Beliakova-Bethell N, Massanella M, White C, Lada SM et al. The effect of cell subset isolation method on gene expression in leukocytes. Cytometry A 2014 Jan;85(1):94-104. PMID: 24115734
  • Microarray
    Illumina HumanHT-12 v4
    50 Samples Loaded: 50
    Human (Homo sapiens)
    CD8 T cells , CD4 T cells , B cells , Monocytes
    Healthy
    Sample Set Spreadsheet
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    Samples Preview
    Sample ID !Sample_title cell type isolation method
    GSM1212208 Donor1_pos_CD4 primary CD4+ T cells Positive selection
    GSM1212209 Donor5_neg_CD8 primary CD8+ T cells Negative selection
    GSM1212210 Donor2_pos_B primary B cells Positive selection
    GSM1212211 Donor3_neg_CD4 primary CD4+ T cells Negative selection
    GSM1212212 Donor4_pos_mono primary monocytes Positive selection
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    Log2 Transformed
    Raw Signal
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    Sample ID !Sample Title Cell type Isolation method
    GSM1212208
    Donor1_pos_CD4
    primary CD4+ T cells
    Positive selection
    GSM1212209
    Donor5_neg_CD8
    primary CD8+ T cells
    Negative selection
    GSM1212210
    Donor2_pos_B
    primary B cells
    Positive selection
    GSM1212211
    Donor3_neg_CD4
    primary CD4+ T cells
    Negative selection
    GSM1212212
    Donor4_pos_mono
    primary monocytes
    Positive selection
    GSM1212213
    Donor3_FACS_B
    primary B cells
    FACS
    GSM1212214
    Donor2_pos_CD8
    primary CD8+ T cells
    Positive selection
    GSM1212215
    Donor4_FACS_CD4
    primary CD4+ T cells
    FACS
    GSM1212216
    Donor4_pos_B
    primary B cells
    Positive selection
    GSM1212217
    Donor4_neg_CD4
    primary CD4+ T cells
    Negative selection
    GSM1212218
    Donor5_neg_B
    primary B cells
    Negative selection
    GSM1212219
    Donor2_pos_CD4
    primary CD4+ T cells
    Positive selection
    GSM1212220
    Donor2_FACS_CD8
    primary CD8+ T cells
    FACS
    GSM1212221
    Donor5_pos_mono
    primary monocytes
    Positive selection
    GSM1212222
    Donor1_FACS_CD4
    primary CD4+ T cells
    FACS
    GSM1212223
    Donor3_neg_CD8
    primary CD8+ T cells
    Negative selection
    GSM1212224
    Donor2_neg_CD4
    primary CD4+ T cells
    Negative selection
    GSM1212225
    Donor3_pos_CD8
    primary CD8+ T cells
    Positive selection
    GSM1212226
    Donor5_neg_mono
    primary monocytes
    Negative selection
    GSM1212227
    Donor3_pos_CD4
    primary CD4+ T cells
    Positive selection
    GSM1212228
    Donor4_FACS_CD8
    primary CD8+ T cells
    FACS
    GSM1212229
    Donor1_pos_mono
    primary monocytes
    Positive selection
    GSM1212230
    Donor3_FACS_CD8
    primary CD8+ T cells
    FACS
    GSM1212231
    Donor3_neg_mono
    primary monocytes
    Negative selection
    GSM1212232
    Donor2_FACS_mono
    primary monocytes
    FACS
    GSM1212233
    Donor5_pos_CD8
    primary CD8+ T cells
    Positive selection
    GSM1212234
    Donor1_FACS_B
    primary B cells
    FACS
    GSM1212235
    Donor4_pos_CD4
    primary CD4+ T cells
    Positive selection
    GSM1212236
    Donor2_neg_B
    primary B cells
    Negative selection
    GSM1212237
    Donor5_FACS_CD4
    primary CD4+ T cells
    FACS
    GSM1212238
    Donor4_neg_CD8
    primary CD8+ T cells
    Negative selection
    GSM1212239
    Donor4_neg_B
    primary B cells
    Negative selection
    GSM1212240
    Donor3_FACS_CD4
    primary CD4+ T cells
    FACS
    GSM1212241
    Donor1_pos_CD8
    primary CD8+ T cells
    Positive selection
    GSM1212242
    Donor5_neg_CD4
    primary CD4+ T cells
    Negative selection
    GSM1212243
    Donor2_pos_mono
    primary monocytes
    Positive selection
    GSM1212244
    Donor2_FACS_B
    primary B cells
    FACS
    GSM1212245
    Donor5_FACS_CD8
    primary CD8+ T cells
    FACS
    GSM1212246
    Donor3_pos_B
    primary B cells
    Positive selection
    GSM1212247
    Donor1_neg_mono
    primary monocytes
    Negative selection
    GSM1212248
    Donor2_FACS_CD4
    primary CD4+ T cells
    FACS
    GSM1212249
    Donor4_pos_CD8
    primary CD8+ T cells
    Positive selection
    GSM1212250
    Donor1_neg_CD4
    primary CD4+ T cells
    Negative selection
    GSM1212251
    Donor3_pos_mono
    primary monocytes
    Positive selection
    GSM1212252
    Donor3_neg_B
    primary B cells
    Negative selection
    GSM1212253
    Donor1_FACS_CD8
    primary CD8+ T cells
    FACS
    GSM1212254
    Donor5_pos_CD4
    primary CD4+ T cells
    Positive selection
    GSM1212255
    Donor2_neg_CD8
    primary CD8+ T cells
    Negative selection
    GSM1212256
    Donor5_pos_B
    primary B cells
    Positive selection
    GSM1212257
    Donor4_neg_mono
    primary monocytes
    Negative selection

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