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Probe Design
- smFISH probes are designed and synthesized by Biosearch Technologies (Petaluma, CA).
- DNA 50mer initiator-labeled oligonucleotide probes were either purchased from Molecular Instruments (Pasadena, CA; Parvalbumin, Tac1, Th), or designed using OligoWiz software (Wernersson et al., 2007) and synthesized by Integrated DNA Technologies (somatostatin, NPY, VIP, Tac2, Malat1, Npas4, Arc).
- LNA probes were synthesized by Exiqon.
mRNA Probe Sequences
Somatostatin
| Probe Type | Amplification Type | Hairpin Set | [Probe] | Accession # | Probe Position | Brain Region |
|---|
| DIG-labled riboprobe | TSA | - | 200ng/ul | BC010770 | 380-429 | Cortex, Hippocampus, Striatum |
| DIG-labeled DNA 50mer | TSA | - | 50nM | | 265, 322, 31 | Cortex, Hippocampus, Striatum |
| 50mer DNA oligonucleotide | HCR | B1 | 4nM | | 265, 322, 31, 430 | Cortex, Hippocampus, Striatum |
| | HCR | B2 | 4nM | | 265, 322, 31, 430 | Cortex, Hippocampus, Striatum |
| | HCR | B5 | 4nM | | 265, 322, 31, 430, 510, 499 | Cortex, Hippocampus, weaker signal makes detection in striatum difficult |
Riboprobe Sequence
- gaatgtcttccagaagaagttcttgcagccagctttgcgttcccggggtg
Oligonucleotide Sequences
- B1 initiator sequences
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgcaaatcctcgggctccagggcatcattctctgtctggttgggctcATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgttcgagttggcagacctctgcagctccagcctcatctcgtcctgctcATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcagccaagctggagcgcggtgggtcagtctagtcgcaggtcctcaATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtccagaagaagttcttgcagccagctttgcgttcccggggtgccaATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- B2 initiator sequences
- CCTCGTAAATCCTCATCAATCATCCAGTAAACCGCCAAAAAgcaaatcctcgggctccagggcatcattctctgtctggttgggctcAAAAAAGCTCAGTCCATCCTCGTAAATCCTCATCAATCATC
- CCTCGTAAATCCTCATCAATCATCCAGTAAACCGCCAAAAAgttcgagttggcagacctctgcagctccagcctcatctcgtcctgctcAAAAAAGCTCAGTCCATCCTCGTAAATCCTCATCAATCATC
- CCTCGTAAATCCTCATCAATCATCCAGTAAACCGCCAAAAAcagccaagctggagcgcggtgggtcagtctagtcgcaggtcctcAAAAAAGCTCAGTCCATCCTCGTAAATCCTCATCAATCATC
- CCTCGTAAATCCTCATCAATCATCCAGTAAACCGCCAAAAAtccagaagaagttcttgcagccagctttgcgttcccggggtgccaAAAAAAGCTCAGTCCATCCTCGTAAATCCTCATCAATCATC
- B5 initiator sequences
- CTCACTCCCAATCTCTATCTACCCTACAAATCCAAT AAAAA gcaaatcctcgggctccagggcatcattctctgtctggttgggctcATTTTCACTTCATATCACTCACTCCCAATCTCTATCTACCC
- CTCACTCCCAATCTCTATCTACCCTACAAATCCAAT AAAAA gttcgagttggcagacctctgcagctccagcctcatctcgtcctgctcATTTTCACTTCATATCACTCACTCCCAATCTCTATCTACCC
- CTCACTCCCAATCTCTATCTACCCTACAAATCCAAT AAAAA cagccaagctggagcgcggtgggtcagtctagtcgcaggtcctcaATTTTCACTTCATATCACTCACTCCCAATCTCTATCTACCC
- CTCACTCCCAATCTCTATCTACCCTACAAATCCAAT AAAAA tccagaagaagttcttgcagccagctttgcgttcccggggtgccaATTTTCACTTCATATCACTCACTCCCAATCTCTATCTACCC
- CTCACTCCCAATCTCTATCTACCCTACAAATCCAAT AAAAA cagtcttcaatttctaatgcagggtcaagttgagcatcgggggccaggATTTTCACTTCATATCACTCACTCCCAATCTCTATCTACCC
- CTCACTCCCAATCTCTATCTACCCTACAAATCCAATAAAAAttcaatttctaatgcagggtcaagttgagcatcgggggccaggagttaaggaagATTTTCACTTCATATCACTCACTCCCAATCTCTATCTACCC
Parvalbumin
| Probe Type | Amplification Type | Hairpin Set | [Probe] | Accession # | Probe Position | Brain Region |
|---|
50mer DNA oligonucleotide | HCR | B1 | 0.5nM | BC027424 | 14, 72, 210, 303 | Cortex, TRN, Cerebellum, weaker in hippocampus |
| | | | | Tested and removed | 400, 473, 683, 762, 550 | |
- B1 initiator probes
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTttcttgatgtcctcagcgctgagcacgtctgtcatcgacatcctgcaact ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtgtctccagcggccagaagcgtctttgtttctttagcagacaagtctctg ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtgtctccagcggccagaagcgtctttgtttctttagcagacaagtctctg AATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtggagaggtgggggacccaagcagtcagcgccacttagctttcagccacc ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- Tested and removed from probe set:
- tacaggtggtgtccgattggtacagcctttattgtttctccagcatttcc
- agtaccaagcaggcaggagatatcggggcgttgtcctttgacttatctca
- aagatggacgatccatcacccccatctccttgtgggaaaggtgcagagat
- ggagtcctttgatctagctagtcctgaaggactcaaccccttcccttccc
- aagaaagaaaaaaaacttgccaaaccaacaccctgccaggcctgggtcct
- Probe Concentration: 200nM
- Hybridization Conditions: 37C, 2xSSC, 40% Formamide
Tachykinin1
| Probe Type | Amplification Type | Hairpin Set | [Probe] | Accession # | Probe Position | Brain Region |
|---|
| 50mer DNA oligonucleotide | HCR | B1 | 2nM | NM_009311 | 250, 441, 528, 799, 874 | Striatum |
- B1 initiator probes:
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTatccaaagaactgctgaggcttgggtcttcgggcgattctctgcagaaga ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtttacgtcttctttcgtagttctgcatcgcgcttctttcataagccacag ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTatcattcctcatagcgcacattttattttaccgttcactgctcactgaca ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTccaggggtagcgtgagagagacgcacaggagtctctgcttccagcagcag ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTacaggaaacatgctgctaggatacaaatagagtcaaataccgaagtctca ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- Probe Concentration: 2nM each
- Hybridization Temperature: 37C
Tachykinin2
| Probe Type | Amplification Type | Hairpin Set | [Probe] | Accession # | Probe Position | Brain Region |
|---|
| 50mer DNA oligonucleotide | HCR | B1 | 1nM | NM_009312.2 | 253, 324, 379 | Cortex, BNST |
| | | | | Tested and removed | 184 | |
- B1 initiator probes:
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtgctcagcactttcagcaatccttccagagagacagggcggctgt ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTccataagtcccacaaagaagtcgtgcatgtcacgtttctgtggaagtga ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- AGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgggtgttctcttcaaccacgtcggtgggagtgtctggttggctgttcc ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- Tested and removed: gaggcagctgatagagatcagagtccttactgagcctccctccct
- Probe Concentration: 2nM each
- Hybridization Temperature: 37C
Tyrosine Hydroxylase
| Probe Type | Amplification Type | Hairpin Set | [Probe] | Accession # | Probe Position | Brain Region |
|---|
| 50mer DNA oligonucleotide | HCR | B1 | 2nM | M69200 | 303, 817, 1277, 1398, 307, 956, 1332, 387, 1158, 514 | Midbrain |
- B1 initiator probes:
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTactctgccgccgtccaatgaaccttggggacgtgacagcctcggcctgct ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTctggaagccagtccgttccttcaagaagtgagacacatcctccagctgtg ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcatcactgaagctctctgacacgaagtacaccggctggtaggtttgatct ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtctaaggagcgccggatggtgtgaggactgtccagtacatcaatggccag ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTccgggtctctaagtggtggattttggcttcaaatgtctcaaacactttca ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgcagctcgtggcagcagtctggctcgggtgagtgcataggtgaggaggcaATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTttcacagagaatgggcgctggatacgagaggcatagttcctgagcttgtcATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgcagccaggtcgccactgggcacctcgaagcgcacaaagtactccaggtgATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTaggagctctccataggaagacagcagccctgcaccgtaagccttcagctcATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTagggtcaaacttggtgaccaggtggtgacacttatccaactctgacacttATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- B2 initiator probes:
- CCTCGTAAATCCTCATCAATCATCCAGTAAACCGCCAAAAAactctgccgccgtccaatgaaccttggggacgtgacagcctcggcctgctATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- CCTCGTAAATCCTCATCAATCATCCAGTAAACCGCCAAAAActggaagccagtccgttccttcaagaagtgagacacatcctccagctgtgATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- CCTCGTAAATCCTCATCAATCATCCAGTAAACCGCCAAAAAAcatcactgaagctctctgacacgaagtacaccggctggtaggtttgatctATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- CCTCGTAAATCCTCATCAATCATCCAGTAAACCGCCAAAAAtctaaggagcgccggatggtgtgaggactgtccagtacatcaatggccagATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- CCTCGTAAATCCTCATCAATCATCCAGTAAACCGCCAAAAAccgggtctctaagtggtggattttggcttcaaatgtctcaaacactttcaATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- CCTCGTAAATCCTCATCAATCATCCAGTAAACCGCCAAAAAgcagctcgtggcagcagtctggctcgggtgagtgcataggtgaggaggcaATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- CCTCGTAAATCCTCATCAATCATCCAGTAAACCGCCAAAAAttcacagagaatgggcgctggatacgagaggcatagttcctgagcttgtcATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- CCTCGTAAATCCTCATCAATCATCCAGTAAACCGCCAAAAAgcagccaggtcgccactgggcacctcgaagcgcacaaagtactccaggtgATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- CCTCGTAAATCCTCATCAATCATCCAGTAAACCGCCAAAAAaggagctctccataggaagacagcagccctgcaccgtaagccttcagctcATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- CCTCGTAAATCCTCATCAATCATCCAGTAAACCGCCAAAAAagggtcaaacttggtgaccaggtggtgacacttatccaactctgacacttATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
Vasoactive Intestinal Peptide
Vasoactive Intestinal Peptide
| Probe Type | Amplification Type | Hairpin Set | [Probe] | Accession # | Probe Position | Brain Region |
|---|
| 50mer DNA oligonucleotide | HCR | B1 | 1nM | NM_011702.3 | 5, 158, 243, 328, 433 | Cortex, Hippocampus, Intestine |
- B1 initiator probes:
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTacactgaagagtatcaggaatgccaggaactgaggcttgcttctggctt ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTattttctgctaagggattctgcaagatgtcagagtctgcttttaaagaga ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTagaaatctgacccagaagtctgctgtaatcgctggtgaaaactccatcagcatgc ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTctcactgctcctctttccattcaggatggagttcaggtatttctt ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgtgtcgtttgattggcacaggatcttccgagatgctgctgctgattcgttt ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- Probe Concentration: 1nM each
- Hybridization Temperature: 37C
Neuropeptide Y
| Probe Type | Amplification Type | Hairpin Set | [Probe] | Accession # | Probe Position | Brain Region |
|---|
| 50mer DNA oligonucleotide | HCR | B1 | 1nM | NM_023456.3 | 21, 134, 218, 398, 451 | Cortex, Hippocampus |
- B1 initiator probes:
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcgtcgctgagcggcgggtgctctgctctgggtgcctctgtgagagaagagatcca ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtggaggggtacccctcagccagaatgcccaaacacacgagcagagatagagcg ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTatgagattgatgtagtgtcgcagagcggagtagtatctggccatgtcctct ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTggggatgagatgagatgagggtggaaacttggaaaagtcgggagaacaagt ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgcggagtccagcctagtggtggcatgcattggtgggacaggcagactggttt ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- Probe Concentration: 1nM each
- Hybridization Temperature: 37C
Malat1
| Probe Type | Amplification Type | Hairpin Set | [Probe] | Accession # | Probe Position | Brain Region |
|---|
| 50mer DNA oligonucleotide | HCR | B1 | 2nM | FJ209304.1 | 461, 1898, 2407, 4598, 6231 | nuclear localized, brain-wide |
- B1 initiator probes:
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTaacgtacatgcgccagtcgaaggatttttataacggccgtcaacttaaccta ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTggctctaccattcattcccctctgagcggttaaagacaacttgccatctaccatt ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTacacactgggttagagaaggcgtgtactgctatgctgttggcacgacacctt ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTaagtgtcttaccctagatgtttagccatggtcaaattagacccctgactt ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTaaccgatatgcaacgtgacctcaaggatccagctactggctgcatcaa ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- Probe Concentration: 2nM each
- Hybridization Temperature: 37C
SERT
- Accession #: NM_010484.2
- B1 initiator probes:
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcattggatatttgtccaggc
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTttgtactgggaactgcggag
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgtagagtgtggcgcttcatc
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgcatagccaatgacagacag
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgggaaaacgccagatgttgc
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcaccattctggtagcatatg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTaaagatggccatgatggtgt
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgagctccatgtagaagagtg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtagaaatgcacccatttcgg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTaaatcgggcagatcttcttc
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgtgttatagtaggaggcgat
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcgtgaaggaggagatgaggt
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtgttccaagagttcttgcag
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcgaagtagttggtgcagttg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTaggtgacgtggaatggagtg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTatggcgcaagtaaaactcct
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTctttgactgatggatctgca
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTatgagcatgatgcagagagc
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTttccagatgctgaagtagat
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcttgccagacgttttgactc
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgccagttgggtttcaagtaa
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTctagcaaacgccaggagaac
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgcatcttggtaacagttgtt
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtcatgcagttcaccacactg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTacaaagccagagacgaagct
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTatgtagccaagcaccgtgaa
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTacacgtcttcgttcctcatc
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcctccgcatatgtgatgaaa
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgcgaacgtactatccaaacc
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcaacacagctgtgatcacac
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcccagatgtgaggaaactca
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcgatgagcacaaaccattcc
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcccaagatgcaagtgatgac
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTctgatgtcagtgtgagcagg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtcgatgagagccacggtgag
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgaaccaagacacgacgacgg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtgcagaactgagtgattcca
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTaaaaccatccggggctgaag
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcaggagaaacagagggctga
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgttggggtggactcatcaaa
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTctccagtggggataattgta
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtatgcagtagcccaagatga
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTagggatgcagatgacagacg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgtgctgatcagccgataaat
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTataatgcgctccttaagtgt
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTggtgtttcaggagtgatact
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTatgtccccacacggaatttc
- Probe Concentration: 2nM each
- Hybridization Temperature:37
Drd2
- Accession #: NM_010077.2
- B1 initiator probes:
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTagatcatcatcgtaccagga
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtggcatagtagttgtagtgg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTaagatgaggagggtgagcag
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgcacattgccaaagacgatg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtctctctggatacagccatg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgttggtggtggtctgcaaag
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTacagcgaggctgactatcag
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTagtgtggccaccagaagatc
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTatagacgacccagggcataa
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTctgctgaatttccactcacc
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgtgacaaagatgtcacagtg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtgtgcacatcatgacatcca
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcaacataggcatggccacag
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtggagctgtagcgtgtgtta
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTatcatgacagtaactcggcg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTaaggacaggacccagacaat
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTaagagcagtgggcaagagat
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTttctggtctgtgttgttgag
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTagggttggcaatgatacact
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtggaggagtagaccacgaag
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgaagggcacgtagaacgaga
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtttgatatagaccagcaggg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgcttgcggagaacgatgtag
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtctgaaagctcggctgctac
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtgagtggtgtcttcaggttg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTagtttcatgtcctcagggtg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTagacttcatgataacggtgc
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtgttcactgggaaactccca
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtgggagggatggggctatac
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgatggatcggggagagtgag
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTttgacaatcttggcatgccc
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTaaagaacttggcaatcctgg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcattgggcatggtctggatc
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtcatcgtcttaagggaggtc
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTaatggcaagcatctgagtgg
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTagccagcagatgatgaacac
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcaggatgtgcgtgatgaaga
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTatgttgcagtcacagtgtat
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgtgcaggatcttcatgaagg
- Probe Concentration: 2nM
- Hybridization Temperature: 37C
Arc
| Probe Type | Amplification Type | Hairpin Set | [Probe] | Accession # | Probe Position | Brain Region Tested |
|---|
| DIG-labled riboprobe | TSA | - | 200ng/ul | BC023127 | entire cDNA | Hippocampus |
| DIG-labeled DNA 50mer | TSA | - | 50nM | | 94, 755, 874, 1295 | Hippocampus |
| 50mer DNA oligonucleotide | HCR | B1 | 2nM | | 877, 208, 330, 1110,94, 755, 874, 1295 | Hippocampus |
DIG-labeled Oligonucleotide Probes
- Probe Sequences
- gccggtgggtcctccgtacgtgttccagcatctcagctcggcacttacc
- tccttcttgaactccacccagttcttcaccgagccctgcttgaactcccaccact
- cccgcttgcgccagaggaactggtcgagtggttcaccctgcttctg
- gctggtaagagcaggtgtgagtgcctccgtctcatcctctgtgggcagtggggtgccag
- Probe concentration: 20nM each
- Hybridization temperature: 60C in 5xSSC + 50% formamide
HCR Probe Sets
- B1 Initiator Probes:
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTaggagcttagcgagtgtggcaggctcgtcgccgctgaagctagagaggccATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtacaggtcccgcttgcgccagaggaactggtcgagtggttcaccctgcttATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcgctgtgagtcgccggtgggcacgtagccgtccaagttgttctccagcttATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcccacctctccagacggtagaagacctccctccacacgtgcatctcacgcATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTactcgctggtaagagcaggtgtgagtgcctccgtctcatcctctgtgggcATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgccggtgggtcctccgtacgtgttccagcatctcagctcggcacttaccATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTtccttcttgaactccacccagttcttcaccgagccctgcttgaactcccaccactATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcccgcttgcgccagaggaactggtcgagtggttcaccctgcttctgATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgctggtaagagcaggtgtgagtgcctccgtctcatcctctgtgggcagtggggtgccagATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- Probe concentration: 0.5nM each
- Hybridization temperature: 37C in 2xSSC + 40% formamide
Npas4
| Probe Type | Amplification Type | Hairpin Set | [Probe] | Accession # | Probe Position | Brain Region Tested |
|---|
| 50mer DNA oligonucleotide | HCR | B1 | 1nM | NM_153553 | 1154, 1889, 1288, 1569, 1032, 1798 | Hippocampus, Cortex |
- B1 Initiator Set:
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgaatgagggtagcacagctggggttcctaggacataggctgcctgg ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTgctgagctagggccaggagtgtacagtccccattaccagggctgcta ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTggagggttggggaagctcttctggtgttgagatcacacctagttcaggag ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcaactgtccttgtagtgaactggttagtgggtctgggaaggtagcactgctggg ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTcagtaaaagggccttctggaccttctgagtatagcatgcagtaaatccatgtcca ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- GAGGAGGGCAGCAAACGGGAAGAGTCTTCCTTTACGATATTctcctgggcgaagtaagtcttggtaggattggggctcagttgctctgggaagg ATATAGCATTCTTTCTTGAGGAGGGCAGCAAACGGGAAGAG
- Probe Concentration: 0.5nM
- Hybridization temperature: 37C
microRNA Probe Sequences
mir-10
- LNA sequence: cacaaattcggttctacagggta
- Hybridization Temperature: 37-55C
- Probe Concentration: 12.5 nM
mir-21
- LNA sequence: tcaacatcagtctgataagcta
- Hybridization Temperature: 37-55C
- Probe Concentration: 12.5nM
mir-124
- LNA sequence: ggcattcaccgcgtgcctta
- Hybridization Temperature: 37-55C
- Probe Concentration: 12.5 nM
mir-128
- LNA sequence: aaagagaccggttcactgtga
- Hybridization Temperature: 37-55C
- Probe Concentration: 12.5 nM
