GEO help: Mouse over screen elements for information.
Status
Public on Jun 21, 2005
Title
NIA Mouse 44K Microarray v2.1 (Whole Genome 60-mer Oligo)
Technology type
in situ oligonucleotide
Distribution
custom-commercial
Organism
Mus musculus Manufacturer
Agilent
Manufacture protocol
As descripted by Agilent manuals under Platform_web_link
Support
glass
Coating
aminosilane
Description
The Agilent's Mouse Development Oligo Microarray 44K is formatted on a 1x3 inch (25mm x 75mm) glass slide. Each 44,290-feature microarray contains 41,034 (60-mer) probes representing all empirical and predicted mouse genes and transcripts from the NIA Mouse Gene Index. The sequence and associated annotation information is based on the NIA Mouse Gene Index 4.0 http://lgsun.grc.nia.nih.gov/geneindex4, which combines genome assembly sequences from public databases (RefSeq, Ensembl, Riken), and the NIA collection of public EST libraries derived from stem cells and early stage of mouse embryos, along with human-curated genetic databases to form structure models of over 40,000 genetic loci4. Furthermore, a set of synthetic spike-in control probes are included to control variations in target labeling and hybridization, and to provide more quantitative information on transcripts5.
Web link
http://www.chem.agilent.com/scripts/generic.asp?lpage=11617&indcol=N&prodcol=Y Submission date
Jun 16, 2005
Last update date
Jan 17, 2013
Contact name
Minoru S.H. Ko
E-mail(s)
kom@mail.nih.gov Phone
410-558-8359
Organization name
NIH
Department
National Institute on Aging
Lab
Lab of Genetics
Street address
251 Bayview Blvd, Suite 100, 10C
City
Baltimore
State/province
MD
ZIP/Postal code
21224
Country
USA
Samples (101)
GSM80055 , GSM80056 , GSM80057 , GSM80058 , GSM80059 , GSM80060
GSM80061 ,
GSM80062 ,
GSM80063 ,
GSM80064 ,
GSM80065 ,
GSM80066 ,
GSM137369 ,
GSM137370 ,
GSM137371 ,
GSM137372 ,
GSM137373 ,
GSM137374 ,
GSM137375 ,
GSM137376 ,
GSM137377 ,
GSM137378 ,
GSM137379 ,
GSM137380 ,
GSM137381 ,
GSM137382 ,
GSM137383 ,
GSM137384 ,
GSM137385 ,
GSM137386 ,
GSM137387 ,
GSM137388 ,
GSM137389 ,
GSM137390 ,
GSM137391 ,
GSM137392 ,
GSM137393 ,
GSM137394 ,
GSM137395 ,
GSM137396 ,
GSM137397 ,
GSM137398 ,
GSM137399 ,
GSM137400 ,
GSM137401 ,
GSM137402 ,
GSM137403 ,
GSM137404 ,
GSM138376 ,
GSM138377 ,
GSM138378 ,
GSM138379 ,
GSM138380 ,
GSM138381 ,
GSM181829 ,
GSM181830 ,
GSM181831 ,
GSM181832 ,
GSM181833 ,
GSM181834 ,
GSM181835 ,
GSM181836 ,
GSM213062 ,
GSM213063 ,
GSM213064 ,
GSM213065 ,
GSM213066 ,
GSM213067 ,
GSM213530 ,
GSM213531 ,
GSM213532 ,
GSM213533 ,
GSM213534 ,
GSM213535 ,
GSM213664 ,
GSM213665 ,
GSM213666 ,
GSM213667 ,
GSM213668 ,
GSM213669 ,
GSM285548 ,
GSM285549 ,
GSM285550 ,
GSM285551 ,
GSM285552 ,
GSM285553 ,
GSM324571 ,
GSM324572 ,
GSM324573 ,
GSM324574 ,
GSM324575 ,
GSM324576 ,
GSM324577 ,
GSM324578 ,
GSM324579 ,
GSM324580 ,
GSM324581 ,
GSM324582 ,
GSM324583 ,
GSM324584 ,
GSM324585 Series (9)
GSE3509 Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray (WGA 2.1 Spike Test)
GSE5914 Global gene expression profiling reveals similarities and differences among mouse pluripotent stem cells
GSE5947 Hematopoietic reconstitution by multipotent adult progenitor cells: precursors to long-term hematopoietic stem cells
GSE7502 Effects of Aging and Calorie Restriction on the Global Gene Expression Profiles of Mouse Testis and Ovary
GSE8583 Gene expression changes in the intestinal crypts of mice with loss of imprinting
GSE8610 Genes regulated by T cell and B cell derived TNF in naive lymph nodes
GSE8617 Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algor
GSE12942 Foxl2 functions in sex determination and histogenesis throughout mouse ovary development, analyzed by Agilent arrays
GSE12989 Foxl2 functions throughout mouse ovary development
Data table header descriptions ID Feature Number
Row Feature location row
Col Feature location column
Start Start position of the probe sequence
ProbeUID Unique integer for each unique probe in a design
ControlType Feature control type 0=Control type none 1=Positive control -1=Negative control -1000=Deletion control -2000=Not probe
ProbeName An Agilent-assigned identifier for the probe synthesized on the microarray
GeneName This is an identifier for the gene for which the probe provides expression information. The target sequence identified by the systematic name is normally a representative or consensus sequence for the gene
OLIGO_NAME NIA Universal Oligo Name
GB_LIST GenBank accession list ,
SPOT_ID SP_LIST SwissProt accession list
SEQUENCE Sequence of oligonucleotide probe
GENE Entrez GENE ID
GENE_SYMBOL Gene symbols Associated with the Oligo, Based on NIA Gene Index 4
GENE_DESCRIPTION Gene Description Based on NIA Gene Index 4
Data table ID Row Col Start ProbeUID ControlType ProbeName GeneName OLIGO_NAME GB_LIST SPOT_ID SP_LIST SEQUENCE GENE GENE_SYMBOL GENE_DESCRIPTION 1
1
1
0
0
1
Pro25G_T10_Pro25G
BrightCorner
Positive Control
ATCATCGTAGCTGGTCAGTGTATCCTTTTTTTTTTATCATCGTAGCTGGTCAGTGTATCC
2
1
3
1
1
-1
(-)3xSLv1
3xSLv1
Negative Control
GCTAGCGAAAGCTAGCTTTTCGATCGGAAACGATCGTTTTCCAGTGACGAAAGTCACTGG
3
1
5
0
2
0
A_66_P125029
NM_021524.1
Z00009690-1
AF234625 , AK004117 , AK086415 , AY679720 , BC004059 , CL302556 CTCCCAGTGTTTAGATGATCTCAGATTAGAAAACACTTACAACCATGTACAAGATTAATG
59027 Pbef1
pre-B-cell colony-enhancing factor 1
4
1
7
0
3
0
A_66_P122529
BC004722
Z00048946-1
AK008790 , AK009681 , AK019083 , AK020134 , AK028133 , AK084336 , AK086443 , AK088913 , BC004722 , BC039749 TCCCCTTAGGTCTGTCTAGAATCCTAAAGGCAGATGACTCAAGGGAACCAGAAAAAAGGA
Ramp2
receptor (calcitonin) activity modifying protein 2
5
1
9
0
4
0
A_66_P123649
AK028297.1
Z00035209-1
AK002569 , AK011350 , AK011750 , AK011838 , AK014265 , AK028297 , AK034725 , AK042804 , AK049682 , BC028847 AAAGGAGCCATTATTGGTTTCCTCAAAGTTGGATACAAGAAGCTCTTTGTACTGGATGAC
73242 2610110G12Rik
RIKEN cDNA 2610110G12 gene
6
1
11
0
5
0
A_66_P121187
XM_287857.1
Z00029122-1
AK018986 GGGCCTGTTTTGGTTTTCTTCATGTTTTCTCTTTCGGGTACCTAGAGACAAGAAAAATAC
Mus musculus 10 days neonate cortex cDNA, RIKEN full-length enriched library, clone:A830006H14 product:unclassifiable, full insert sequence.
7
1
13
0
6
1
Pro25G_EQCP1_T5
QC_Fusion
Positive Control
_____ATCATCGTAGCTGGTCAGTGTATCCGGTCAGTGTATCCAGTTTCTCCGAATTTTT
8
1
15
0
7
0
A_66_P108681
ENSMUST00000060098
Z00046994-1
GTGTGGCCTTTCCCGACTTTACCCATAGATAAATTTTTAGCAATTTTCGATGCCATTATC
258440 Olfr1317
olfactory receptor 1317
9
1
17
0
8
0
A_66_P127908
BB631670.1
Z00064845-1
TATGGTGTACACCTTTAATGCCAACACTCTGGGAGTCAGAGAGGCAAGTGGATCTCAGAG
10
1
19
0
9
0
A_66_P112956
XM_149230.1
Z00054387-1
AK013301 GCTGTTGCTATGGTAACAACGGCTTAAGAGCCTTAGGCCCCCCTCTGGGGTGACAGGCTT
1700060C20Rik
RIKEN cDNA 1700060C20 gene
11
1
21
120
10
1
r60_a20
r60_a20
Positive Control
CGGAACCACCTGGAGCTCGATCTAGTCCCTAAAGGGGGGGAGCAGGGATTTGCTAAGCTT
12
1
23
0
11
0
A_66_P101510
AK018308.1
Z00028159-1
AK011145 TTGGAAACTCAACGAATGAGAGCATCCACCTTTTGTTTCCACGTGAAAACATGTACTTGA
6530401F13Rik
RIKEN cDNA 6530401F13 gene
13
1
25
0
12
0
A_66_P104062
AK033132
Z00052857-1
AK009772 , AK017750 , AK041787 CTATATGTTCTAGTCCAGCTATTGAGGGGTATAAGACAATTTTTCATTCTAGTAGCAATG
2310043D08Rik,5730505K17Rik
RIKEN cDNA 2310043D08 gene
14
1
27
0
6
1
Pro25G_EQCP1_T5
QC_Fusion
Positive Control
_____ATCATCGTAGCTGGTCAGTGTATCCGGTCAGTGTATCCAGTTTCTCCGAATTTTT
15
1
29
0
13
0
A_66_P111898
NM_145997.1
Z00035074-1
AK035270 , AK040260 , AK046187 , BC010717 , BC011506 , BC025481 CATAAGAAAGATTTGATTGAATTGAGAGTAATGCTGGAAGATGCTGAGGATAGGAAATAC
214899 Jarid1a
jumonji, AT rich interactive domain 1A (Rbp2 like)
16
1
31
0
14
0
A_66_P115274
NM_172894.2
Z00056203-1
AK075825 , AK080891 , AK020143 TCAGCTCCTGCTTGAGCCTCCCAAGCTGGAGCCTCTGCAGATGACGTGGGGCAGTCTGGC
243819 B430201G11Rik
RIKEN cDNA B430201G11 gene
17
1
33
0
15
0
A_66_P128773
BC027567
Z00044941-1
AY158688 GCAAGTAGACATAAATCACATTAACTAGGACTCATCACCAATTCATCAGTGATCCTGTTT
Mus musculus, clone IMAGE:3472070, mRNA.
18
1
35
0
16
0
A_66_P103150
BC024705
Z00047357-1
AK006786 , AK082235 , AK086180 , BC024705 , AF208120 TTTTTACTTTGGGTTCTTGAGTATGATAATTTCTAGAATGCAGACTGACTTCATTCCACG
1700054N08Rik
RIKEN cDNA 1700054N08 gene
19
1
37
0
17
0
A_66_P134349
M77196.1
Z00014831-1
AF101164 , AK085749 , BC016891 , BC024320 , M61907 , M77196 , M96934 , X15351 , X53084 , X67279 P31809
TAGCCCCTCAAGCCCTTTTGATCATGAGTTCCAAACCAAAAATAAATAAATGAACAGTGA
26365 Ceacam2,Ceacam1
CEA-related cell adhesion molecule 2
20
1
39
0
18
0
A_66_P111038
Z00069007-1
Z00069007-1
GAAGCTGTAGAAGATATCTGGTTACTACAGCAGCATTGTAGGTGTTCCCTGGTCTGCTCA
43430 8055 Kbytes .Supplementary data files not provided
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