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Series GSE1870 Query DataSets for GSE1870
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.




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Supplementary data files not provided

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