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Platform GPL1010 Query DataSets for GPL1010
Status Public on Oct 26, 2004
Title MPSS [DpnII: Mus musculus] signature list
Technology type MPSS
Distribution virtual
Organism Mus musculus
Description MPSS signatures detected in Lynx mouse transcriptome analysis experiment.

To generate a complete, annotated mouse signature database, we extracted all the possible signatures (“virtual signatures”) from the mouse genome sequence (NCBI build 33) and the mouse UniGene sequences (UniGene build #145). Each virtual signature is ranked based on its position and orientation in the original sequence. The annotation for that sequence is then assigned to the signature and the resulting signature database is used to annotate the data from the experiments, using our “TopHit” algorithm.

Virtual Signature Class| mRNA Orientation| Poly-Adenelation| Features| Position
0 Either - Repeat Warning Not applicable Not applicable
1 Forward Strand Poly-A Signal, Poly-A Tail 3' most
2 Forward Strand Poly-A Signal 3' most
3 Forward Strand Poly-A Tail 3' most
4 Forward Strand None 3' most
5 Forward Strand None Not 3' most
6 Forward Strand Internal Poly-A Not 3' most
11 Reverse Strand Poly-A Signal, Poly-A Tail 5' most
12 Reverse Strand Poly-A Signal 5' most
13 Reverse Strand Poly-A Tail 5' most
14 Reverse Strand None 5' most
15 Reverse Strand None Not 5' most
16 Reverse Strand Internal Poly-A Not 3' most
22 Unknown Poly-A Signal Last before signal
23 Unknown Poly-A Tail Last before tail
24 Unknown None Last in sequence
25 Unknown None Not last
26 Unknown Internal Poly-A Not 3' most
1000 Unknown - Derived from Genomic Sequence Not applicable Not applicable
Contributor(s) Vasicek T, Khrebtukova I, Zhou D
Submission date Feb 25, 2004
Last update date Mar 16, 2006
Contact name Daixing Zhou
Phone 510-670-9441
Fax 510-670-9302
Organization name Solexa
Department Bioinformatics
Street address 25861 Industrial Blvd
City Hayward
State/province CA
ZIP/Postal code 94545
Country USA
Samples (93) GSM17228, GSM17241, GSM17242, GSM17243, GSM17244, GSM17245 
Series (2)
GSE1067 MPSS analysis of mouse BLK CL.4 and liver cells
GSE1581 MPSS mouse transcriptome analysis project

Data table header descriptions
ID Signature (20 bp sequence including DpnII site GATC)
SEQ_ID Sequence ID
SIG_CLASS Signature class
SPOT_ID Text description for all other signatures
CLUSTER_SIZE Number of transcripts in the UniGene cluster (for the signatures with UniGene annotation)
GB_ACC GenBank accession
DESCRIPTION UniGene cluster title for the signatures with Unigene annotation

Data table
GATCTCTGTGCAGTTCAAAA Mm.273578 3 109 BC004056 Transmembrane protein 34
GATCCTCTCGTGGCTTCCTA Mm.122399 1 158 BC090651 CDNA sequence BC030863
GATCTTGATTGAATGTGATA Mm.257266 1 168 CO040854 Eph receptor A7
GATCCTCTCCGATGGGGAAC Mm.270278 4 544 AY540632 Thyrotroph embryonic factor
GATCTCTGTGAGTTGAAGGC Mm.295013 4 285 AK047228 Vacuolar protein sorting 11 (yeast)
GATCCTTCACAGACGAGAGA Mm.40537 4 66 AA645002 RIKEN cDNA A830021K08 gene
GATCCCTCAAGAACAGAAAA Mm.253067 4 218 BB652899 Myelin transcription factor 1-like
GATCTAGCTGAGTTTTTACA Mm.332919 3 157 BC062926 Forkhead box P2
GATCTCTGTGAGGTACAGCA Mm.196275 3 250 BC067054 RIKEN cDNA 4930535B03 gene
GATCTGACACATCTGGAGTG Mm.65979 22 365 AI593332 RIKEN cDNA 5730526G10 gene
GATCCTCTATGGACACTAAC Mm.229107 4 289 AK182165 RIKEN cDNA C530043G21 gene
GATCCCACCACTAAAAACTA Mm.22480 22 372 AV230641 Cyclin D binding myb-like transcription factor 1
GATCTCTGTCATTTGGAGCC Mm.297784 2 32 AI314836 Gene model 850, (NCBI)
GATCCTTATACACCACAACG Mm.99793 3 198 BC042733 RIKEN cDNA 1110007C24 gene
GATCTGACACACCCCCTTTG Mm.6877 2 193 AK078414 Adaptor protein complex AP-2, alpha 1 subunit
GATCCCACACATCCTGAAAG Mm.271222 4 1044 AW044940 Eukaryotic translation initiation factor 5
GATCTCTGGTGTCATGGTGG Mm.278643 1 341 NM_153563 RIKEN cDNA 6330569M22 gene
GATCTGACAAGCCACAGTGT Mm.237966 2 98 NM_172760 Engulfment and cell motility 3, ced-12 homolog (C. elegans)
GATCTGACAAAGGACACCAA Mm.318259 4 222 BU582901 Fas-associated factor 1
GATCTGAATGGGAGGTATTT Mm.182769 4 183 AI172765 RNA binding motif protein 17

Total number of rows: 71752

Table truncated, full table size 5799 Kbytes.

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Supplementary data files not provided

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