GEO help: Mouse over screen elements for information.
Status
Public on Oct 28, 2004
Title
Bovine blood gamma/delta T cell stimulation study
Organism
Bos taurus
Experiment type
Expression profiling by array
Summary
Blood gamma/delta T cells were purfiied from holstein calves less than six months old. Blood from 4 individual calves were pooled and gamma/delta T cells were purified by immunomagnetic separation, rested in RPMI medium for 12h, and underwent ConA & hIL-2 stimulation. Total RNAs were extracted by using Trizol reagents. 15 ug of total RNA was used for cDNA synthesis and microarray hybridization. Table 1: regulated genes These genes were identified, in GeneSpring software, via filtering of genes with relative expression ratio of 1.5 and over or 0.667 or below, equivalent to up- and down-regulation by fold change 1.5 or more, in both experiments. Table 2: down-regulated genes These genes were identified, in GeneSpring software, via filtering of genes with relative expression ratio of 0.667 or below, equivalent to down-regulation by fold change 1.5 or more, in both experiments. The avergae fold change was then converted to negative value. Gene annotation was performed by using GeneSpring's "Build Simplified Ontology" constructor. Table 3: up-regulated genes These genes were identified, in GeneSpring software, via filtering of genes with relative expression ratio of 1.5 or over, equivalent to up-regulation by fold change 1.5 or more, in both samples. Gene annotation was performed by using GeneSpring's "Build Simplified Ontology" constructor. Keywords: other
Contributor(s)
Deng M , Liu J , Lancto CA , Pelak CN , Abrahamsen M
Citation missing
Has this study been published? Please login to update or notify GEO .
Submission date
Oct 22, 2004
Last update date
Mar 15, 2012
Contact name
Mingqi Deng
E-mail(s)
dengx010@umn.edu
Phone
612-625-7737
Fax
612-625-0204
Organization name
University of Minnesota
Department
Veterinary and Biomedical Sciences
Lab
Mitchell Abrahamsen
Street address
1988 Fitch Avenue
City
Saint Paul
State/province
MN
ZIP/Postal code
55108
Country
USA
Platforms (1)
GPL1527
CattleArray3800 from PyxisGenomics
Samples (2)
GSM33123
Bovine blood gamma/delta T cell stimulation: exp1 data
GSM33124
Bovine blood gamma/delta T cell stimulation: exp2 data
Relations
BioProject
PRJNA90541
Table 1: regulated genes header descriptions
ID_REF
VALUE
average fold change
Value-exp1
fold change in exp1
Value-exp2
fold change in exp2
Common
gene symbol
Genbank
GenBank accession number
Gene Description
Unigene description of top hit
Data table
ID_REF
VALUE
Value-exp1
Value-exp2
Common
Genbank
Gene Description
28
0.620023072
0.42174554
0.6200231
TMSB4X
BG495020
"thymosin, beta 4, X chromosome"
173
1.584140778
1.7564957
1.5841408
ARPC5
BF792619
"actin related protein 2/3 complex, subunit 5 (16 kD)"
174
1.725677848
1.778544
1.7256778
ARPC5
BF792619
"actin related protein 2/3 complex, subunit 5 (16 kD)"
241
1.575143576
1.6854098
1.5751436
286
0.634700656
0.62079823
0.63470066
TMSB10
AI718269
"thymosin, beta 10"
423
1.524356246
3.1504366
1.5243562
PPP1CA
M63960
"protein phosphatase 1, catalytic subunit, alpha isoform"
537
1.512300849
2.4152272
1.5123008
607
0.586152256
0.5575394
0.58615226
Y14372
adducin 3 (gamma)
626
1.953953266
2.068254
1.9539533
ID2
D13891
"inhibitor of DNA binding 2, dominant negative helix-loop-helix protein"
671
0.498559445
0.45755935
0.49855945
BG257623
SH3 domain binding glutamic acid-rich protein like 3
672
0.567032218
0.46262088
0.5670322
BG257623
SH3 domain binding glutamic acid-rich protein like 3
676
1.546419978
2.0971668
1.54642
HRY
AF264785
hairy (Drosophila)-homolog
707
1.977692485
2.1380951
1.9776925
AW965236
"molecule possessing ankyrin repeats induced by lipopolysaccharide (MAIL), homolog of mouse"
708
1.696948886
1.7777779
1.6969489
AW965236
"molecule possessing ankyrin repeats induced by lipopolysaccharide (MAIL), homolog of mouse"
837
1.548942685
2.4916842
1.5489427
AL576815
protein disulfide isomerase-related protein
838
1.585093379
2.1103513
1.5850934
AL576815
protein disulfide isomerase-related protein
847
1.551374435
3.9035485
1.5513744
848
1.648657084
3.7152708
1.6486571
871
1.579581738
3.0562832
1.5795817
TRA1
NM_003299
tumor rejection antigen (gp96) 1
872
1.585069299
2.7574453
1.5850693
TRA1
NM_003299
tumor rejection antigen (gp96) 1
Total number of rows: 158 Table truncated, full table size 12 Kbytes .Table 2: down-regulated genes header descriptions
ID_REF
VALUE
average fold change (converted)
Value-exp1
fold change in exp1
Value-exp2
fold change in exp2
Value-ave
average fold change
Genbank
GenBank accession number
Gene Description
Unigene description of top hit
Annotation
gene annotation
Data table
ID_REF
VALUE
Value-exp1
Value-exp2
Value-ave
Genbank
Gene Description
Annotation
7355
-3.45
0.29
0.2
0.39
AW239219
annexin A1
"cell growth, apoptosis, anti-inflammatory"
6479
-3.23
0.31
0.2
0.42
AL522954
protein kinase C-like 1
1775
-3.03
0.33
0.22
0.44
BE393934
glutathione peroxidase 1
inhibition of CD95-induced apoptosis
7540
-3.03
0.33
0.16
0.5
AL527803
high-mobility group (nonhistone chromosomal) protein 2
7415
-2.86
0.35
0.29
0.42
AW966520
"ESTs, Weakly similar to 2109260A B cell growth factor [H.sapiens]"
signal transducer
4858
-2.7
0.37
0.36
0.39
AL544550
transgelin 2
cell movement and cytoskeletal organization
6503
-2.7
0.37
0.27
0.46
AV763203
ribosomal protein S29
4464
-2.5
0.4
0.31
0.49
AF161506
HSPC157 protein
stress response
6405
-2.38
0.42
0.35
0.49
BF568447
amino-terminal enhancer of split
6173
-2.22
0.45
0.42
0.47
BG528861
ribosomal protein L10
1877
-2.22
0.45
0.42
0.48
AL133642
RNB6
2887
-2.17
0.46
0.33
0.59
BF111865
"thymosin, beta 4, X chromosome"
cell movement and cytoskeletal organization
4198
-2.13
0.47
0.35
0.6
671
-2.08
0.48
0.46
0.5
BG257623
SH3 domain binding glutamic acid-rich protein like 3
cell movement and cytoskeletal organization
4953
-2.08
0.48
0.4
0.57
BC005080
immediate early response 3
"cell growth, apoptosis"
3382
-2.08
0.48
0.36
0.6
X57985
"H2B histone family, member Q"
4248
-2.08
0.48
0.36
0.61
BG535318
"actin related protein 2/3 complex, subunit 3 (21 kD)"
cell movement and cytoskeletal organization
4210
-2.08
0.48
0.33
0.63
7563
-2
0.5
0.47
0.52
BF790073
"CD47 antigen (Rh-related antigen, integrin-associated signal transducer)"
signal transduction
7411
-2
0.5
0.45
0.54
BG252389
"ESTs, Highly similar to B27079 fibronectin receptor beta chain precursor [H.sapiens]"
"cell communication, cell movement"
Total number of rows: 66 Table truncated, full table size 5 Kbytes .Table 3: up-regulated genes header descriptions
ID_REF
VALUE
average fold change
Value-exp1
fold change in exp1
Value-exp2
fold change in exp2
Genbank
genBank accession number
Gene Description
Unigene description of top hit
Annotation
gene annotation
Data table
ID_REF
VALUE
Value-exp1
Value-exp2
Genbank
Gene Description
Annotation
1851
4.26
4.87
3.66
BC001263
serum/glucocorticoid regulated kinase
1875
4.03
4.86
3.21
AB043885
"basic helix-loop-helix domain containing, class B, 2"
cell growth and differentiation
3960
3.27
4.43
2.1
BG476500
"eukaryotic translation initiation factor 4A, isoform 1"
translational control
4004
2.83
3.3
2.37
BG681954
"heat shock 90kD protein 1, beta"
stress response
847
2.73
3.9
1.55
3923
2.6
2.97
2.23
NM_022073
EGL nine (C.elegans) homolog 3
"regulation of growth, differentiation"
7920
2.58
3.58
1.59
7869
2.51
3.11
1.92
BE296065
KIAA1415 protein
unknown
7906
2.38
2.27
2.48
BE537595
hypothetical protein FLJ23476
7327
2.34
2.45
2.23
BG742704
3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble)
cholesterol biosynthesis
7400
2.34
2.96
1.73
BF772928
"cadherin 1, type 1, E-cadherin (epithelial)"
cell communication
423
2.34
3.15
1.52
M63960
"protein phosphatase 1, catalytic subunit, alpha isoform"
cell growth
871
2.32
3.06
1.58
NM_003299
tumor rejection antigen (gp96) 1
stress response
1518
2.23
2.93
1.54
2913
2.21
2.9
1.53
BF035373
fatty acid binding protein 5 (psoriasis-associated)
metabolism
6950
2.13
2.69
1.58
6895
2.07
2.53
1.62
707
2.06
2.14
1.98
AW965236
"molecule possessing ankyrin repeats induced by lipopolysaccharide (MAIL), homolog of mouse"
regulation of inflammatory responses
7845
2.06
2.23
1.88
BG775493
jumping translocation breakpoint
involved in an unbalanced jumping translocation (unbalanced translocation that comprises amplified chromosomal segments jumping to various telomeres)
1940
2.05
2.57
1.52
Total number of rows: 42 Table truncated, full table size 2 Kbytes .
Supplementary data files not provided