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Status
Public on Aug 04, 2015
Title
[BovGene-1_1-st] Bovine Gene 1.1 ST Array [transcript (gene) version]
Technology type
in situ oligonucleotide
Distribution
commercial
Organism
Bos taurus
Manufacturer
Affymetrix
Manufacture protocol
See manufacturer's web site
Description
Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html Platform table create dwith Affymetrix annotation file BovGene-1_1-st-v1.na34.umd3.transcript.csv: #%create_date=Wed Apr 2 10:16:16 2014 PDT #%chip_type=BovGene-1_1-st-v1 #%lib_set_name=BovGene-1_1-st #%lib_set_version=v1 #%genome-version=umd3 #%genome-version-ucsc=umd3 #%genome-lifted-method=psl-map.pl #%genome-lifted_from-version-ucsc=umd3 #%netaffx-annotation-date=2013-08-30 #%netaffx-annotation-netaffx-build=34
Web link
http://www.affymetrix.com/support/technical/byproduct.affx?product=modelorg_1_1_array http://www.affymetrix.com/support/technical/libraryfilesmain.affx
Submission date
Aug 04, 2015
Last update date
Aug 04, 2015
Organization
Affymetrix, Inc.
E-mail(s)
geo@ncbi.nlm.nih.gov, support@affymetrix.com
Phone
888-362-2447
URL
http://www.affymetrix.com/index.affx
Street address
City
Santa Clara
State/province
CA
ZIP/Postal code
95051
Country
USA
Samples (194)
GSM1843279 , GSM1843280 , GSM1843281 , GSM1843282 , GSM1843283 , GSM1843284
GSM1843285 ,
GSM1843286 ,
GSM1843287 ,
GSM1843288 ,
GSM1843289 ,
GSM1843290 ,
GSM1843291 ,
GSM1843292 ,
GSM1843293 ,
GSM1843294 ,
GSM1843295 ,
GSM1843296 ,
GSM1843297 ,
GSM1843298 ,
GSM1843299 ,
GSM1843300 ,
GSM1843301 ,
GSM1843302 ,
GSM1887838 ,
GSM1887839 ,
GSM1887840 ,
GSM1887841 ,
GSM1887842 ,
GSM1887843 ,
GSM1887844 ,
GSM1887845 ,
GSM1887846 ,
GSM1887847 ,
GSM1887848 ,
GSM1887849 ,
GSM1887850 ,
GSM1887851 ,
GSM1887852 ,
GSM1887853 ,
GSM1887854 ,
GSM1887855 ,
GSM1887856 ,
GSM1887857 ,
GSM1887858 ,
GSM1887859 ,
GSM1887860 ,
GSM1887861 ,
GSM1887862 ,
GSM1887863 ,
GSM1887864 ,
GSM1887865 ,
GSM1887866 ,
GSM1887867 ,
GSM1887868 ,
GSM1887869 ,
GSM1887870 ,
GSM1887871 ,
GSM1887872 ,
GSM1887873 ,
GSM1887874 ,
GSM1887875 ,
GSM1887876 ,
GSM1887877 ,
GSM1887878 ,
GSM1887879 ,
GSM1887880 ,
GSM1887881 ,
GSM1887882 ,
GSM1887883 ,
GSM1887884 ,
GSM1887885 ,
GSM1889796 ,
GSM1889797 ,
GSM1889798 ,
GSM1889799 ,
GSM1889800 ,
GSM1889801 ,
GSM1889802 ,
GSM1889803 ,
GSM1889804 ,
GSM1889805 ,
GSM1889806 ,
GSM1889807 ,
GSM1889808 ,
GSM1889809 ,
GSM1889810 ,
GSM1889811 ,
GSM1901075 ,
GSM1901076 ,
GSM1901077 ,
GSM1901078 ,
GSM1901079 ,
GSM1901080 ,
GSM1901081 ,
GSM1901082 ,
GSM1901083 ,
GSM1901084 ,
GSM1901085 ,
GSM1901086 ,
GSM1901087 ,
GSM1901088 ,
GSM1901089 ,
GSM1964315 ,
GSM1964316 ,
GSM1964317 ,
GSM1964318 ,
GSM1964319 ,
GSM1964320 ,
GSM1964321 ,
GSM1964322 ,
GSM1964323 ,
GSM1964324 ,
GSM1964325 ,
GSM1964326 ,
GSM1964327 ,
GSM1964328 ,
GSM1964329 ,
GSM1964330 ,
GSM2068759 ,
GSM2068760 ,
GSM2068761 ,
GSM2068762 ,
GSM2068763 ,
GSM2068764 ,
GSM2068765 ,
GSM2068766 ,
GSM2068767 ,
GSM2068768 ,
GSM2068769 ,
GSM2068770 ,
GSM2068771 ,
GSM2068772 ,
GSM2068773 ,
GSM2068774 ,
GSM2482014 ,
GSM2482015 ,
GSM2482016 ,
GSM2482017 ,
GSM2482018 ,
GSM2482019 ,
GSM2482020 ,
GSM2482021 ,
GSM2482022 ,
GSM2482023 ,
GSM2482024 ,
GSM2482025 ,
GSM2482026 ,
GSM2482027 ,
GSM2482028 ,
GSM2482029 ,
GSM2482030 ,
GSM2482031 ,
GSM2482032 ,
GSM2482033 ,
GSM2482034 ,
GSM2482035 ,
GSM2482036 ,
GSM2482037 ,
GSM2482778 ,
GSM2482779 ,
GSM2482780 ,
GSM2482781 ,
GSM2482782 ,
GSM2482783 ,
GSM2482784 ,
GSM2482785 ,
GSM2482786 ,
GSM2482787 ,
GSM2482788 ,
GSM2482789 ,
GSM2482790 ,
GSM2482791 ,
GSM2482792 ,
GSM2482793 ,
GSM2482794 ,
GSM2482795 ,
GSM2482796 ,
GSM2482797 ,
GSM2482798 ,
GSM2482799 ,
GSM2482800 ,
GSM2482801 ,
GSM3444382 ,
GSM3444383 ,
GSM3444384 ,
GSM3444385 ,
GSM3444386 ,
GSM3444387 ,
GSM3444388 ,
GSM3444389 ,
GSM3444390 ,
GSM3444391 ,
GSM3444392
Series (9)
GSE71696
Influence of bovine virus diarrhoea virus on the transcriptome profile of bovine endometrium in response to bacterial lipopolysaccharide.
GSE73159
Differential gene expression in the duodenum, jejunum, and ileum among crossbred beef steers with divergent gain and feed intake phenotypes.
GSE73261
Differential gene expression in the spleen among crossbred beef steers with divergent gain and feed intake phenotypes.
GSE73699
Differential gene expression in the mesenteric fat among crossbred beef steers with divergent gain and feed intake phenotypes
GSE75700
Differential gene expression in the liver among crossbred beef steers with divergent gain and feed intake phenotypes
GSE78173
Mammary gland transcriptome study in heifers
GSE94746
Differential gene expression in the adipose tissue of crossbred beef cows with divergent gain after feed restriction and ad libitum feeding studies.
GSE94777
Differential gene expression in the muscle tissue of crossbred beef cows with divergent gain after feed restriction and ad libitum feeding studies.
GSE121715
Preweaning nutrient supply alters mammary gland transcriptome expression relating to morphology, lipid accumulation, DNA synthesis and RNA expression in Holstein heifer calves.
Data table header descriptions
ID
transcript_cluster_id
probeset_id
Unique identifier for the probe set.
seqname
chromosome number
strand
(+|-)
start
(integer). Coordinates are standard 1-based (length=stop-start+1).
stop
(integer). Coordinates are standard 1-based (length=stop-start+1).
SPOT_ID
GB_ACC
SPOT_ID
total_probes
Total number of probes contained by this transcript cluster.
gene_assignment
Gene name(s) for each assigned mRNA for mRNAs that corresponds to known genes. (multipart)
mrna_assignment
Public mRNAs that should be detected by this probe set based on sequence alignment determined at the time of the current NetAffx annotation update. (multipart).
swissprot
unigene
category
Array design category of the transcript cluster
Data table
ID
probeset_id
seqname
strand
start
stop
SPOT_ID
GB_ACC
SPOT_ID
total_probes
gene_assignment
mrna_assignment
swissprot
unigene
category
12678162
12678162
chr1
+
52363681
52364912
chr1(+):52363681-52364912
NM_001105490
26
NM_001105490 // CCDC54 // coiled-coil domain containing 54 // --- // 100125920 /// ENSBTAT00000063186 // CCDC54 // coiled-coil domain containing 54 // --- // 100125920 /// BC114016 // CCDC54 // coiled-coil domain containing 54 // --- // 100125920
NM_001105490 // RefSeq // Bos taurus coiled-coil domain containing 54 (CCDC54), mRNA. // chr1 // 100 // 100 // 26 // 26 // 0 /// ENSBTAT00000063186 // ENSEMBL // cdna:known chromosome:UMD3.1:1:52363681:52364911:1 gene:ENSBTAG00000046313 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 26 // 26 // 0 /// BC114016 // GenBank // Bos taurus coiled-coil domain containing 54, mRNA (cDNA clone MGC:137076 IMAGE:8009238), complete cds. // chr1 // 100 // 100 // 26 // 26 // 0
NM_001105490 // Q29RU3 /// ENSBTAT00000063186 // Q29RU3 /// BC114016 // Q29RU3
NM_001105490 // Bt.97953 // liver| testis| calf /// ENSBTAT00000063186 // Bt.97953 // liver| testis| calf /// BC114016 // Bt.97953 // liver| testis| calf
main
12678166
12678166
chr1
+
123009129
123060130
chr1(+):123009129-123060130
NM_001105506
22
NM_001105506 // PLSCR1 // phospholipid scramblase 1 // --- // 100125943 /// ENSBTAT00000044362 // PLSCR1 // phospholipid scramblase 1 // --- // 100125943 /// BC149269 // PLSCR1 // phospholipid scramblase 1 // --- // 100125943
NM_001105506 // RefSeq // Bos taurus phospholipid scramblase 1 (PLSCR1), mRNA. // chr1 // 100 // 100 // 22 // 22 // 0 /// ENSBTAT00000044362 // ENSEMBL // cdna:known chromosome:UMD3.1:1:123009129:123060090:1 gene:ENSBTAG00000031306 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 22 // 22 // 0 /// BC149269 // GenBank // Bos taurus phospholipid scramblase 1, mRNA (cDNA clone MGC:148322 IMAGE:8044257), complete cds. // chr1 // 100 // 100 // 22 // 22 // 0
NM_001105506 // A6QPD9 /// ENSBTAT00000044362 // E1BK12 /// ENSBTAT00000044362 // A6QPD9 /// BC149269 // A6QPD9
NM_001105506 // Bt.50321 // liver| calf /// ENSBTAT00000044362 // Bt.50321 // liver| calf /// BC149269 // Bt.50321 // liver| calf
main
12678175
12678175
chr1
+
41953493
41956764
chr1(+):41953493-41956764
XM_001788046
21
XM_001788046 // LOC100137810 // uncharacterized LOC100137810 // --- // 100137810 /// ENSBTAT00000032401 // LOC100137810 // uncharacterized LOC100137810 // --- // 100137810
XM_001788046 // RefSeq // PREDICTED: Bos taurus uncharacterized LOC100137810 (LOC100137810), mRNA. // chr1 // 100 // 100 // 21 // 21 // 0 /// ENSBTAT00000032401 // ENSEMBL // cdna:known chromosome:UMD3.1:1:41955547:41957126:1 gene:ENSBTAG00000023668 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 38 // 8 // 8 // 0
ENSBTAT00000032401 // E1BFC7
---
main
12678178
12678178
chr1
+
74466956
74470640
chr1(+):74466956-74470640
BC142078
28
BC142078 // LOC100138235 // glypican 5-like // --- // 100138235
BC142078 // GenBank // Bos taurus cDNA clone IMAGE:8066625. // chr1 // 100 // 100 // 28 // 28 // 0
---
BC142078 // Bt.71312 // liver| calf
main
12678183
12678183
chr1
+
4955364
4956425
chr1(+):4955364-4956425
XM_001787777
22
XM_001787777 // KRTAP24-1 // keratin associated protein 24-1 // --- // 100138320 /// ENSBTAT00000063306 // KRTAP24-1 // keratin associated protein 24-1 // --- // 100138320
XM_001787777 // RefSeq // PREDICTED: Bos taurus keratin associated protein 24-1 (KRTAP24-1), mRNA. // chr1 // 100 // 100 // 22 // 22 // 0 /// ENSBTAT00000063306 // ENSEMBL // cdna:known chromosome:UMD3.1:1:4955536:4956408:1 gene:ENSBTAG00000046384 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 91 // 20 // 20 // 0 /// GENSCAN00000005146 // ENSEMBL // cdna:genscan chromosome:UMD3.1:1:4955364:4956326:1 transcript_biotype:protein_coding // chr1 // 100 // 59 // 13 // 13 // 0
ENSBTAT00000063306 // G3N073
ENSBTAT00000063306 // Bt.104320 // skin|fetus
main
12678186
12678186
chr1
+
65718095
65720164
chr1(+):65718095-65720164
GENSCAN00000043173
23
---
GENSCAN00000043173 // ENSEMBL // cdna:genscan chromosome:UMD3.1:1:65706905:65720114:1 transcript_biotype:protein_coding // chr1 // 100 // 83 // 19 // 19 // 0
---
---
main
12678189
12678189
chr1
+
84326119
84525728
chr1(+):84326119-84525728
XM_002684886
23
XM_002684886 // MCF2L2 // MCF.2 cell line derived transforming sequence-like 2 // --- // 100139125 /// ENSBTAT00000013720 // MCF2L2 // MCF.2 cell line derived transforming sequence-like 2 // --- // 100139125
XM_002684886 // RefSeq // PREDICTED: Bos taurus MCF.2 cell line derived transforming sequence-like 2 (MCF2L2), mRNA. // chr1 // 100 // 100 // 23 // 23 // 0 /// ENSBTAT00000013720 // ENSEMBL // cdna:known chromosome:UMD3.1:1:84324970:84525526:1 gene:ENSBTAG00000010394 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 23 // 23 // 0 /// GENSCAN00000004450 // ENSEMBL // cdna:genscan chromosome:UMD3.1:1:84329580:84415400:1 transcript_biotype:protein_coding // chr1 // 100 // 39 // 9 // 9 // 0 /// GENSCAN00000004454 // ENSEMBL // cdna:genscan chromosome:UMD3.1:1:84444265:84509466:1 transcript_biotype:protein_coding // chr1 // 100 // 17 // 4 // 4 // 0
ENSBTAT00000013720 // F1MQ44
XM_002684886 // Bt.66611 // --- /// ENSBTAT00000013720 // Bt.66611 // ---
main
12678219
12678219
chr1
+
64552411
64559966
chr1(+):64552411-64559966
ENSBTAT00000018814
24
ENSBTAT00000018814 // BT.61788 // --- // --- // ---
ENSBTAT00000018814 // ENSEMBL // cdna:known chromosome:UMD3.1:1:64552516:64557030:1 gene:ENSBTAG00000014157 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 92 // 22 // 22 // 0
ENSBTAT00000018814 // F1MMA3
---
main
12678223
12678223
chr1
+
76850454
77001495
chr1(+):76850454-77001495
ENSBTAT00000066200
27
ENSBTAT00000066200 // GMNC // geminin coiled-coil domain containing // --- // 100139788
ENSBTAT00000066200 // ENSEMBL // cdna:known chromosome:UMD3.1:1:76996347:77001495:1 gene:ENSBTAG00000023593 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 44 // 12 // 12 // 0
ENSBTAT00000066200 // G3MXZ4
---
main
12678232
12678232
chr1
+
158171126
158172898
chr1(+):158171126-158172898
XR_083440
18
XR_083440 // LOC100139888 // heterogeneous nuclear ribonucleoproteins C1/C2-like // --- // 100139888
XR_083440 // RefSeq // PREDICTED: Bos taurus heterogeneous nuclear ribonucleoproteins C1/C2-like (LOC100139888), miscRNA. // chr1 // 85 // 72 // 11 // 13 // 0 /// GENSCAN00000035439 // ENSEMBL // cdna:genscan chromosome:UMD3.1:1:158120993:158172724:1 transcript_biotype:protein_coding // chr1 // 100 // 28 // 5 // 5 // 0
---
XR_083440 // Bt.104370 // testis
main
12678235
12678235
chr1
+
95201065
95206791
chr1(+):95201065-95206791
ENSBTAT00000052461
23
ENSBTAT00000052461 // ZSCAN23 // --- // --- // ---
ENSBTAT00000052461 // ENSEMBL // cdna:known chromosome:UMD3.1:1:95203732:95206770:1 gene:ENSBTAG00000037965 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 70 // 16 // 16 // 0
ENSBTAT00000052461 // E1BBS4
---
main
12678240
12678240
chr1
+
82540596
82550283
chr1(+):82540596-82550283
XM_002684871
10
XM_002684871 // LOC100140254 // tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide-like // --- // 100140254
XM_002684871 // RefSeq // PREDICTED: Bos taurus tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide-like (LOC100140254), mRNA. // chr1 // 100 // 100 // 10 // 10 // 0 /// GENSCAN00000007301 // ENSEMBL // cdna:genscan chromosome:UMD3.1:1:82531895:82550013:1 transcript_biotype:protein_coding // chr1 // 100 // 100 // 10 // 10 // 0
---
---
main
12678244
12678244
chr1
+
96642034
96642735
chr1(+):96642034-96642735
GENSCAN00000044354
25
---
GENSCAN00000044354 // ENSEMBL // cdna:genscan chromosome:UMD3.1:1:96601847:96675917:1 transcript_biotype:protein_coding // chr1 // 100 // 100 // 25 // 25 // 0
---
---
main
12678246
12678246
chr1
+
59371394
59387525
chr1(+):59371394-59387525
XM_002684782
23
XM_002684782 // TIGIT // T cell immunoreceptor with Ig and ITIM domains // --- // 100140801 /// ENSBTAT00000015813 // TIGIT // T cell immunoreceptor with Ig and ITIM domains // --- // 100140801
XM_002684782 // RefSeq // PREDICTED: Bos taurus T cell immunoreceptor with Ig and ITIM domains (TIGIT), mRNA. // chr1 // 100 // 100 // 23 // 23 // 0 /// ENSBTAT00000015813 // ENSEMBL // cdna:known chromosome:UMD3.1:1:59371394:59387525:1 gene:ENSBTAG00000011921 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 23 // 23 // 0 /// GENSCAN00000037586 // ENSEMBL // cdna:genscan chromosome:UMD3.1:1:59368218:59375625:1 transcript_biotype:protein_coding // chr1 // 100 // 78 // 18 // 18 // 0
ENSBTAT00000015813 // E1BF67
---
main
12678251
12678251
chr1
+
4893265
4895000
chr1(+):4893265-4895000
BC119911
24
BC119911 // KRTAP27-1 // keratin associated protein 27-1 // --- // 100141020
BC119911 // GenBank // Bos taurus cDNA clone IMAGE:8284388, partial cds. // chr1 // 100 // 100 // 24 // 24 // 0
BC119911 // Q0VCZ9
BC119911 // Bt.75698 // skin|fetus
main
12678254
12678254
chr1
+
45021286
45044430
chr1(+):45021286-45044430
EF432552
8
EF432552 // PRDM9 // PR domain containing 9 // --- // 100190914
EF432552 // GenBank // Bos taurus chromosome 1 PR domain zinc finger protein 9 (PRDM9) mRNA, PRDM9-meisetz allele, partial cds. // chr1 // 100 // 38 // 3 // 3 // 0
EF432552 // A3RLY6
EF432552 // Bt.100752 // ---
main
12678266
12678266
chr1
+
93789331
93798359
chr1(+):93789331-93798359
XM_002683605
10
XM_002683605 // LOC100294973 // aTP-binding cassette, sub-family C (CFTR/MRP), member 4-like // --- // 100294973
XM_002683605 // RefSeq // PREDICTED: Bos taurus aTP-binding cassette, sub-family C (CFTR/MRP), member 4-like (LOC100294973), mRNA. // chr1 // 100 // 100 // 10 // 10 // 0 /// GENSCAN00000002190 // ENSEMBL // cdna:genscan chromosome:UMD3.1:1:93714961:94025141:1 transcript_biotype:protein_coding // chr1 // 100 // 30 // 3 // 3 // 0
---
---
main
12678271
12678271
chr1
+
77415804
77436595
chr1(+):77415804-77436595
ENSBTAT00000017899
28
ENSBTAT00000017899 // TMEM207 // transmembrane protein 207 // --- // 100295666 /// XM_002702440 // TMEM207 // transmembrane protein 207 // --- // 100295666
ENSBTAT00000017899 // ENSEMBL // cdna:known chromosome:UMD3.1:1:77415804:77436583:1 gene:ENSBTAG00000013456 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 28 // 28 // 0 /// XM_002702440 // RefSeq // PREDICTED: Bos taurus transmembrane protein 207 (TMEM207), mRNA. // chr1 // 93 // 100 // 26 // 28 // 0 /// GENSCAN00000028901 // ENSEMBL // cdna:genscan chromosome:UMD3.1:1:77427716:77436466:1 transcript_biotype:protein_coding // chr1 // 100 // 29 // 8 // 8 // 0
ENSBTAT00000017899 // E1B7Y0
ENSBTAT00000017899 // Bt.99286 // kidney| calf /// XM_002702440 // Bt.99286 // kidney| calf
main
12678279
12678279
chr1
+
152898001
152899476
chr1(+):152898001-152899476
GENSCAN00000003915
17
---
GENSCAN00000003915 // ENSEMBL // cdna:genscan chromosome:UMD3.1:1:152898001:152930229:1 transcript_biotype:protein_coding // chr1 // 100 // 94 // 16 // 16 // 0
---
---
main
12678281
12678281
chr1
+
4693604
4703336
chr1(+):4693604-4703336
XM_002702416
8
XM_002702416 // LOC100296223 // uncharacterized LOC100296223 // --- // 100296223
XM_002702416 // RefSeq // PREDICTED: Bos taurus uncharacterized LOC100296223 (LOC100296223), mRNA. // chr1 // 100 // 100 // 8 // 8 // 0
---
---
main
Total number of rows: 26773 Table truncated, full table size 22888 Kbytes .
Supplementary data files not provided