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Clinical

Transcriptome analysis of HIV-infected peripheral blood monocytes - GSE50011

Purpose

Immunologic dysfunction, mediated via monocyte activity, has been implicated in the development of HIV-associated neurocognitive disorder (HAND). We hypothesized that transcriptome changes in peripheral blood monocytes relate to neurocognitive functioning in HIV+ individuals, and that such alterations could be useful as biomarkers of worsening HAND. METHODS: mRNA was isolated from the monocytes of 86 HIV+ adults and analyzed with the Illumina HT-12 v4 Expression BeadChip. Neurocognitive functioning, HAND diagnosis, and other clinical and virologic variables were determined.

Hypothesis

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Experimental Design

mRNA was isolated from the monocytes of 86 HIV+ adults and analyzed with the Illumina HT-12 v4 Expression BeadChip. Neurocognitive functioning, HAND diagnosis, and other clinical and virologic variables were determined.

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
86 Samples Loaded: 86
Human (Homo sapiens)
Monocytes
HIV, Neurological disorders
Sample Set Spreadsheet
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Samples Preview
Sample ID !Sample Title Age Weight batch race
GSM1212268 PBMC_1 61 83.1 1 1
GSM1212269 PBMC_2 54 81 1 1
GSM1212270 PBMC_3 43 1 8
GSM1212271 PBMC_4 49 73.2 1 2
GSM1212272 PBMC_5 62 88.8 1 1
Please log in in order to upload files.
File
sampleset4000021_sampleannotations.csv
Sample Set Spreadsheet
sampleset4000021_sampleannotations.csv
Sample Set Spreadsheet
Log2 Transformed
Raw Signal
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Samples Viewer / Editor

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Sample ID !Sample Title Age Weight Batch Race Height Artdate Cocaine Anycancer Smoke Alcohol Bmi Hivdate Vload Cell type VL group Cannabis CD4 count CD4 count group CNS penetration group Date of closest visit Depression scale Developmental stage Disease state History Of Cns Opport Inf History Of Hiv-assoc Neurol Disease Nadir CD4 count YRS from seroconv YRS from seroconv group
GSM1212268
PBMC_1
61
83.1
1
1
1.727
1/15/94
None
0
2
None
27.9
11/10/91
29
Peripheral blood monocytes
20-600
None
576
>500
3
10/8/11
0
adult
HIV+
0
0
282
19.91
16-28
GSM1212269
PBMC_2
54
81
1
1
1.88
7/14/06
None
0
2
None
22.9
8/1/03
10
Peripheral blood monocytes
0
None
532
>500
3
10/15/11
20
adult
HIV+
0
0
320
8.21
1-10
GSM1212270
PBMC_3
43
 
1
8
1.702
3/22/03
None
0
1
None
 
11/13/02
10
Peripheral blood monocytes
0
Daily
713
>500
4
10/17/11
48
adult
HIV+
0
0
235
8.93
1-10
GSM1212271
PBMC_4
49
73.2
1
2
1.829
10/19/98
None
0
2
Monthly
21.9
4/10/02
10
Peripheral blood monocytes
0
None
865
>500
4
11/15/11
8
adult
HIV+
0
1
486
9.6
1-10
GSM1212272
PBMC_5
62
88.8
1
1
1.93
2/20/98
None
0
1
Daily
23.8
12/14/89
10
Peripheral blood monocytes
0
None
215
<500
3
11/16/11
1
adult
HIV+
1
1
176
21.92
16-28
GSM1212273
PBMC_6
53
 
1
1
1.803
2/16/92
None
0
1
Weekly
 
5/3/84
10
Peripheral blood monocytes
0
None
688
>500
4
11/16/11
6
adult
HIV+
0
1
262
27.54
16-28
GSM1212274
PBMC_7
52
82.8
1
1
1.626
10/1/89
None
0
1
None
31.3
8/29/84
10
Peripheral blood monocytes
0
None
476
<500
3
11/16/11
3
adult
HIV+
1
0
114
27.21
16-28
GSM1212275
PBMC_8
52
76.9
1
2
1.778
12/22/95
None
0
2
None
24.3
11/10/94
10
Peripheral blood monocytes
0
None
631
>500
3
11/23/11
9
adult
HIV+
0
0
56
17.03
16-28
GSM1212276
PBMC_9
38
 
1
2
1.651
1/17/02
None
0
2
Monthly
 
4/15/02
10
Peripheral blood monocytes
0
Daily
369
<500
3
11/29/11
2
adult
HIV+
0
0
227
9.62
1-10
GSM1212277
PBMC_10
54
106
1
1
1.727
9/4/10
None
0
2
Weekly
35.5
3/10/10
10
Peripheral blood monocytes
0
None
673
>500
3
11/30/11
2
adult
HIV+
0
0
341
1.72
1-10
GSM1212278
PBMC_11
63
76.7
1
1
1.803
1/23/96
 
1
 
 
23.6
1/30/85
10
Peripheral blood monocytes
0
 
610
>500
3
12/17/11
 
adult
HIV+
0
0
108
26.88
16-28
GSM1212279
PBMC_12
65
51.9
1
1
1.702
8/8/88
None
0
2
None
17.9
5/22/84
10
Peripheral blood monocytes
0
Monthly
405
<500
4
1/4/12
15
adult
HIV+
1
1
1
27.62
16-28
GSM1212280
PBMC_13
67
85.7
1
1
1.778
7/5/97
None
0
2
None
27.1
7/19/94
10
Peripheral blood monocytes
0
None
851
>500
4
1/7/12
3
adult
HIV+
0
1
301
17.47
16-28
GSM1212281
PBMC_14
58
87.9
1
1
1.753
4/16/92
None
0
1
Weekly
28.6
6/14/84
10
Peripheral blood monocytes
0
Weekly
843
>500
3
1/7/12
6
adult
HIV+
0
0
401
27.56
16-28
GSM1212282
PBMC_15
60
67.2
1
1
1.778
10/25/95
None
0
2
Daily
21.3
4/17/85
10
Peripheral blood monocytes
0
None
751
>500
3
1/11/12
3
adult
HIV+
0
0
281
26.74
16-28
GSM1212283
PBMC_16
51
79
1
1
1.778
4/23/97
None
0
2
None
25
9/7/84
10
Peripheral blood monocytes
0
None
786
>500
4
1/19/12
6
adult
HIV+
0
0
188
27.36
16-28
GSM1212284
PBMC_17
62
88.3
1
1
1.803
10/13/89
None
0
1
Weekly
27.2
7/28/84
10
Peripheral blood monocytes
0
None
513
>500
3
1/13/12
 
adult
HIV+
0
1
267
27.46
16-28
GSM1212285
PBMC_18
59
87.2
1
1
1.803
11/13/88
None
0
2
None
26.8
8/7/84
10
Peripheral blood monocytes
0
None
465
<500
4
2/2/12
19
adult
HIV+
0
0
200
27.49
16-28
GSM1212286
PBMC_19
44
90.4
1
8
1.778
11/30/99
None
0
1
None
28.6
1/7/03
33
Peripheral blood monocytes
20-600
None
648
>500
3
2/7/12
39
adult
HIV+
0
0
425
9.08
1-10
GSM1212287
PBMC_20
42
 
1
2
1.524
1/1/87
None
0
2
None
 
4/1/02
10
Peripheral blood monocytes
0
None
717
>500
3
11/30/11
0
adult
HIV+
0
1
384
9.66
1-10
GSM1212288
PBMC_21
40
 
1
8
1.626
10/4/03
None
0
3
None
 
10/22/02
10
Peripheral blood monocytes
0
None
911
>500
3
12/1/11
19
adult
HIV+
0
1
465
9.11
1-10
GSM1212289
PBMC_22
43
74
1
2
1.651
8/13/05
None
0
1
None
27.1
4/18/02
10
Peripheral blood monocytes
0
None
762
>500
3
12/6/11
13
adult
HIV+
0
0
401
9.63
1-10
GSM1212290
PBMC_23
59
88.8
1
1
1.727
10/4/08
None
0
2
Daily
29.8
10/19/84
10
Peripheral blood monocytes
0
None
718
>500
3
12/9/11
11
adult
HIV+
0
1
432
27.14
16-28
GSM1212291
PBMC_24
63
83.6
1
1
1.88
12/10/89
None
0
2
Monthly
23.7
1/22/85
10
Peripheral blood monocytes
0
Monthly
576
>500
3
12/10/11
4
adult
HIV+
0
0
116
26.88
16-28
GSM1212292
PBMC_25
55
 
1
2
1.803
1/1/87
None
0
3
Weekly
 
3/20/03
10
Peripheral blood monocytes
0
Daily
398
<500
3
12/13/11
10
adult
HIV+
0
0
114
8.73
1-10
GSM1212293
PBMC_26
50
93.2
1
1
1.753
2/4/93
None
0
1
None
30.3
10/25/84
36
Peripheral blood monocytes
20-600
Daily
598
>500
4
12/14/11
19
adult
HIV+
0
0
222
27.13
16-28
GSM1212294
PBMC_27
49
 
1
2
1.829
4/12/01
None
0
2
None
 
3/19/03
94
Peripheral blood monocytes
20-600
Monthly
693
>500
3
12/14/11
29
adult
HIV+
1
0
336
8.74
1-10
GSM1212295
PBMC_28
67
89
1
1
1.88
3/17/90
None
0
2
Weekly
25.2
9/7/89
10
Peripheral blood monocytes
0
None
338
<500
3
12/15/11
9
adult
HIV+
0
0
92
22.27
16-28
GSM1212296
PBMC_29
46
 
1
8
1.753
1/1/87
None
0
2
None
 
7/22/02
2840
Peripheral blood monocytes
>1000
None
493
<500
3
10/18/11
12
adult
HIV+
0
0
209
9.24
1-10
GSM1212297
PBMC_30
61
67.9
1
1
1.753
6/18/87
None
0
2
Monthly
22.1
9/25/84
10
Peripheral blood monocytes
0
None
470
<500
4
10/19/11
6
adult
HIV+
0
0
10
27.06
16-28
GSM1212298
PBMC_31
64
92.5
1
1
1.778
12/22/97
None
0
3
Monthly
29.3
8/21/84
10
Peripheral blood monocytes
0
Daily
762
>500
3
10/19/11
47
adult
HIV+
0
1
366
27.16
16-28
GSM1212299
PBMC_32
55
89.9
1
1
1.854
12/31/96
None
0
3
Weekly
26.1
8/21/84
10
Peripheral blood monocytes
0
None
147
<500
4
10/22/11
18
adult
HIV+
0
0
98
27.17
16-28
GSM1212300
PBMC_33
58
86.7
1
1
1.854
11/3/93
None
1
2
Daily
25.2
11/2/84
10
Peripheral blood monocytes
0
Daily
371
<500
3
10/22/11
6
adult
HIV+
0
0
72
26.97
16-28
GSM1212301
PBMC_34
49
83.9
1
1
1.854
7/18/94
None
0
3
None
24.4
6/29/84
10
Peripheral blood monocytes
0
None
910
>500
4
10/22/11
5
adult
HIV+
1
0
431
27.31
16-28
GSM1212302
PBMC_35
62
59.1
1
2
1.651
6/13/93
None
0
2
None
21.7
9/15/84
10
Peripheral blood monocytes
0
None
513
>500
3
10/26/11
29
adult
HIV+
0
1
329
27.11
16-28
GSM1212303
PBMC_36
64
84.8
1
1
1.829
1/31/95
None
0
2
None
25.4
5/25/84
303
Peripheral blood monocytes
20-600
None
360
<500
2
11/4/11
0
adult
HIV+
0
1
119
27.44
16-28
GSM1212304
PBMC_37
31
 
2
8
1.727
1/19/06
None
0
2
Monthly
 
2/9/05
26200
Peripheral blood monocytes
>1000
Weekly
850
>500
3
1/25/12
17
adult
HIV+
0
0
668
6.96
1-10
GSM1212305
PBMC_38
60
51.7
2
1
1.753
11/9/98
None
0
2
Monthly
16.8
8/16/84
10
Peripheral blood monocytes
0
None
524
>500
2
1/26/12
13
adult
HIV+
0
0
30
27.44
16-28
GSM1212306
PBMC_39
37
 
2
2
1.803
4/20/11
None
0
2
Weekly
 
4/22/02
10
Peripheral blood monocytes
0
Weekly
303
<500
3
1/27/12
0
adult
HIV+
0
1
264
9.77
1-10
GSM1212307
PBMC_40
60
84.6
2
3
1.803
 
None
0
2
None
26
2/6/85
11900
Peripheral blood monocytes
>1000
Daily
441
<500
 
1/28/12
34
adult
HIV+
0
1
257
26.97
16-28
GSM1212308
PBMC_41
49
78
2
1
1.803
5/4/94
None
0
1
None
24
8/23/84
10
Peripheral blood monocytes
0
None
490
<500
3
2/1/12
19
adult
HIV+
0
1
86
27.44
16-28
GSM1212309
PBMC_42
55
88
2
2
1.702
3/20/90
None
0
3
None
30.4
5/12/84
10
Peripheral blood monocytes
0
None
299
<500
3
2/2/12
0
adult
HIV+
0
1
21
27.73
16-28
GSM1212310
PBMC_43
49
 
2
3
1.727
3/1/04
None
0
3
None
 
6/10/03
70
Peripheral blood monocytes
20-600
Weekly
317
<500
3
2/6/12
3
adult
HIV+
0
1
17
8.66
1-10
GSM1212311
PBMC_44
63
 
2
1
1.829
11/23/92
None
0
1
Weekly
 
8/21/84
10
Peripheral blood monocytes
0
Weekly
384
<500
4
2/8/12
5
adult
HIV+
0
0
55
27.47
16-28
GSM1212312
PBMC_45
59
88.6
2
1
1.702
4/30/02
Weekly
0
2
Monthly
30.6
5/23/01
10
Peripheral blood monocytes
0
Weekly
1091
>500
3
2/11/12
9
adult
HIV+
0
0
233
10.72
1-10
GSM1212313
PBMC_46
51
92.5
2
1
1.727
12/16/89
None
0
2
Daily
31
11/7/84
10
Peripheral blood monocytes
0
None
717
>500
3
2/11/12
17
adult
HIV+
0
0
316
27.26
16-28
GSM1212314
PBMC_47
34
86.6
2
2
1.727
2/25/00
None
0
2
None
29
7/29/02
10
Peripheral blood monocytes
0
None
487
<500
3
3/6/12
21
adult
HIV+
0
0
7
9.6
1-10
GSM1212315
PBMC_48
42
 
2
8
1.651
12/14/02
None
0
2
None
 
9/14/02
10
Peripheral blood monocytes
0
None
828
>500
4
3/7/12
12
adult
HIV+
1
1
298
9.48
1-10
GSM1212316
PBMC_49
40
 
2
2
1.702
1/1/87
None
0
2
None
 
2/14/03
10
Peripheral blood monocytes
0
None
671
>500
2
3/7/12
25
adult
HIV+
0
1
439
9.06
1-10
GSM1212317
PBMC_50
38
 
2
8
1.753
2/15/02
None
0
3
Monthly
 
8/15/02
156000
Peripheral blood monocytes
>1000
Daily
564
>500
3
3/8/12
34
adult
HIV+
0
0
272
9.56
1-10
GSM1212318
PBMC_51
54
102
2
1
1.778
6/28/96
None
0
3
Monthly
32.3
1/16/85
10
Peripheral blood monocytes
0
None
365
<500
3
3/8/12
27
adult
HIV+
0
1
107
27.14
16-28
GSM1212319
PBMC_52
60
124.5
2
3
1.88
2/15/99
None
0
2
None
35.2
4/26/03
10
Peripheral blood monocytes
0
None
751
>500
3
3/10/12
13
adult
HIV+
0
0
556
8.87
1-10
GSM1212320
PBMC_53
51
90.1
2
1
1.905
10/13/96
None
0
3
None
24.8
1/30/85
10
Peripheral blood monocytes
0
None
561
>500
4
3/10/12
22
adult
HIV+
0
1
414
27.11
16-28
GSM1212321
PBMC_54
50
94.6
2
1
1.829
7/28/90
None
0
2
Daily
28.3
11/28/84
10
Peripheral blood monocytes
0
None
605
>500
3
3/17/12
29
adult
HIV+
0
1
357
27.3
16-28
GSM1212322
PBMC_55
61
99.7
2
1
1.803
1/4/88
None
0
2
None
30.7
1/14/85
10
Peripheral blood monocytes
0
None
450
<500
3
3/23/12
11
adult
HIV+
0
1
232
27.19
16-28
GSM1212323
PBMC_56
49
69.8
2
8
1.702
12/3/02
None
0
3
Monthly
24.1
4/23/03
10
Peripheral blood monocytes
0
None
739
>500
3
3/29/12
2
adult
HIV+
0
0
64
8.93
1-10
GSM1212324
PBMC_57
48
79.9
2
8
1.676
12/1/99
None
0
1
Monthly
28.4
7/24/02
10
Peripheral blood monocytes
0
None
517
>500
3
2/16/12
0
adult
HIV+
0
0
309
9.57
1-10
GSM1212325
PBMC_58
49
55
2
8
1.6
1/1/87
None
0
3
None
21.5
4/7/03
10
Peripheral blood monocytes
0
None
534
>500
3
2/22/12
8
adult
HIV+
0
0
20
8.88
1-10
GSM1212326
PBMC_59
51
70.1
2
1
1.727
12/3/90
Weekly
0
3
None
23.5
8/31/84
10
Peripheral blood monocytes
0
Weekly
509
>500
3
2/22/12
3
adult
HIV+
0
0
282
27.48
16-28
GSM1212327
PBMC_60
31
 
2
8
1.651
4/29/08
None
0
3
Monthly
 
5/1/03
616
Peripheral blood monocytes
20-600
None
73
<500
3
2/24/12
24
adult
HIV+
0
1
33
8.82
1-10
GSM1212328
PBMC_61
60
65
2
3
1.727
1/21/95
None
1
1
None
21.8
7/11/92
10
Peripheral blood monocytes
0
None
403
<500
3
2/25/12
4
adult
HIV+
0
0
188
19.62
16-28
GSM1212329
PBMC_62
58
60.4
2
1
1.753
9/9/92
None
1
2
None
19.7
4/13/85
10
Peripheral blood monocytes
0
None
828
>500
4
2/29/12
16
adult
HIV+
0
1
13
26.88
16-28
GSM1212330
PBMC_63
53
 
2
8
1.753
5/11/01
None
0
2
None
 
2/6/03
10
Peripheral blood monocytes
0
None
713
>500
3
3/1/12
14
adult
HIV+
0
0
225
9.07
1-10
GSM1212331
PBMC_64
52
89.3
2
1
1.88
12/15/88
None
0
2
None
25.3
11/21/84
10
Peripheral blood monocytes
0
None
812
>500
3
3/3/12
7
adult
HIV+
0
1
181
27.28
16-28
GSM1212332
PBMC_65
50
76.7
2
1
1.778
3/15/90
None
0
2
Monthly
24.3
1/30/85
29
Peripheral blood monocytes
20-600
None
685
>500
3
3/3/12
26
adult
HIV+
0
0
407
27.09
16-28
GSM1212333
PBMC_66
62
70.1
2
1
1.829
5/14/88
None
0
3
Monthly
21
7/21/84
10
Peripheral blood monocytes
0
Weekly
615
>500
3
3/3/12
0
adult
HIV+
0
0
361
27.62
16-28
GSM1212334
PBMC_67
51
84.7
2
1
1.854
12/21/87
None
0
1
Daily
24.6
9/13/84
10
Peripheral blood monocytes
0
Daily
783
>500
3
3/3/12
0
adult
HIV+
0
0
184
27.47
16-28
GSM1212335
PBMC_68
37
68.6
2
2
1.753
1/1/87
None
0
1
Monthly
22.3
7/16/02
110
Peripheral blood monocytes
20-600
None
488
<500
3
11/28/11
42
adult
HIV+
0
0
456
9.37
1-10
GSM1212336
PBMC_69
49
103.2
2
1
1.803
1/19/97
None
0
1
Daily
31.7
1/22/96
10
Peripheral blood monocytes
0
Daily
1012
>500
3
11/30/11
36
adult
HIV+
0
0
522
15.85
16-28
GSM1212337
PBMC_70
53
65.4
2
1
1.727
4/8/04
None
1
1
None
21.9
6/20/84
10
Peripheral blood monocytes
0
None
326
<500
3
12/1/11
31
adult
HIV+
0
0
93
27.45
16-28
GSM1212338
PBMC_71
66
85.3
2
1
1.753
9/13/92
None
0
2
None
27.8
5/18/84
32
Peripheral blood monocytes
20-600
None
609
>500
3
12/8/11
0
adult
HIV+
0
1
452
27.56
16-28
GSM1212339
PBMC_72
32
 
2
8
1.702
5/7/06
None
0
3
Daily
 
4/9/03
10
Peripheral blood monocytes
0
None
642
>500
3
1/3/12
29
adult
HIV+
0
0
194
8.74
1-10
GSM1212340
PBMC_73
48
84.2
2
1
1.829
10/26/95
None
0
2
None
25.2
3/28/94
10
Peripheral blood monocytes
0
None
786
>500
3
1/7/12
21
adult
HIV+
0
0
275
17.78
16-28
GSM1212341
PBMC_74
59
63.3
2
1
1.778
10/31/96
None
0
2
Daily
20
2/25/85
10
Peripheral blood monocytes
0
Daily
955
>500
3
1/13/12
 
adult
HIV+
0
1
383
26.88
16-28
GSM1212342
PBMC_75
55
77.5
2
1
1.778
9/16/90
None
0
3
Daily
24.5
6/27/84
22
Peripheral blood monocytes
20-600
Monthly
435
<500
4
1/14/12
21
adult
HIV+
0
0
211
27.55
16-28
GSM1212343
PBMC_76
51
106.1
2
3
1.88
4/30/10
None
0
2
None
30
4/3/90
10
Peripheral blood monocytes
0
Daily
 
>500
3
1/21/12
4
adult
HIV+
0
0
564
21.8
16-28
GSM1212344
PBMC_77
30
111.9
2
3
1.854
 
None
0
1
Monthly
32.5
1/10/08
583
Peripheral blood monocytes
20-600
None
670
>500
 
1/23/12
4
adult
HIV+
0
1
285
4.04
1-10
GSM1212345
PBMC_78
42
88.1
2
2
1.676
9/18/01
None
0
1
None
31.3
7/25/02
10
Peripheral blood monocytes
0
None
432
<500
3
1/24/12
10
adult
HIV+
0
0
170
9.5
1-10
GSM1212346
PBMC_79
63
57
2
1
1.702
11/15/95
None
0
3
None
19.7
1/26/85
10
Peripheral blood monocytes
0
None
472
<500
3
10/5/11
1
adult
HIV+
0
0
78
26.69
16-28
GSM1212347
PBMC_80
61
74.7
2
1
1.803
1/21/95
None
0
2
None
23
2/12/85
10
Peripheral blood monocytes
0
None
613
>500
3
10/5/11
1
adult
HIV+
0
0
383
26.64
16-28
GSM1212348
PBMC_81
32
 
2
8
1.676
7/14/11
 
0
1
 
 
3/27/03
1160
Peripheral blood monocytes
>1000
 
338
<500
3
10/6/11
 
adult
HIV+
0
0
339
8.53
1-10
GSM1212349
PBMC_82
33
72.6
2
8
1.702
10/13/02
None
0
2
Monthly
25.1
12/11/02
10
Peripheral blood monocytes
0
None
639
>500
4
10/19/11
26
adult
HIV+
0
0
294
8.85
1-10
GSM1212350
PBMC_83
49
78.8
2
3
1.778
8/24/92
None
0
2
Weekly
24.9
1/25/85
10
Peripheral blood monocytes
0
None
497
<500
3
11/5/11
27
adult
HIV+
0
0
44
26.78
16-28
GSM1212351
PBMC_84
54
73.9
2
1
1.829
8/3/94
None
0
1
Monthly
22.1
8/23/93
10
Peripheral blood monocytes
0
None
635
>500
3
11/10/11
10
adult
HIV+
0
1
266
18.21
16-28
GSM1212352
PBMC_85
42
76.6
2
3
1.803
 
None
0
2
None
23.6
12/4/02
11700
Peripheral blood monocytes
>1000
None
528
>500
 
11/21/11
12
adult
HIV+
0
0
382
8.96
1-10
GSM1212353
PBMC_86
60
62.5
2
1
1.727
 
None
0
2
Daily
21
5/23/84
26400
Peripheral blood monocytes
>1000
None
568
>500
 
11/23/11
1
adult
HIV+
0
1
348
27.5
16-28

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