Table 1.
List of Primer Sequences Used for Gene Expression Analysis and Molecular Cloning
| Gene | Forward primer | Reverse primer | Product (bp) |
|---|---|---|---|
| Primers used for RT-PCR and Q-PCR analysis
| |||
| Aldolase | 5′-AGCTGTCTGACATCGCTCACCG-3′ | 5′-CACATACTGGCAGCGCTTCAAG-3′ | 571 |
| m_β-actin | 5′-CTACGAGGGCTATGCTCTCCC-3′ | 5′-CCGGACTCATCGTACTCCTGC-3′ | 602 |
| CSPG2 | 5′-GCCTTCAGTTCAGTAGACAGACTTC-3′ | 5′-AGTAGCATTTGCACACTCTTCTTCT-3′ | 573 |
| CSPG3 | 5′-TGCAACTACAACCTACCCTATGTCT-3′ | 5′-ACTCTCTTGTTTCTCTCTGGGTTCT-3′ | 460 |
| CSPG4 | 5′-GGGTCTGAGGATCTGGTCTACA-3′ | 5′-CTCATACAGAATATTCCCAGCGTAG-3′ | 465 |
| h_EGR-1 | 5′-CGGCAGAAGGACAAGAAAGCAGAC-3′ | 5′-GGGGAAGTGGGCAGAAAGGATTG-3′ | 561 |
| m_Egr-1 | 5′-CGAACAACCCTATGAGCACCTG-3′ | 5′-CAGAGGAAGACGATGAAGCAGC-3′ | 276 |
| m_Egr-1 genotype | 5′-AGGCTCTTAATACCACCTACCAATC-3′ | 5′-TTTCTTGTCCTTCTGTCTTAAATGG-3′ | 362 |
| m_Egr-2 | 5′-CCCAGTAACTCTCAGTGGTTTTATG-3′ | 5′-ATTGATGATACCTTCTGGATAGCAG-3′ | 313 |
| m_Egr-3 | 5′-CCATTACAATCAGATGGCTACAG-3′ | 5′-TAGTCAGGAATCATGGGGAAAAGAT-3′ | 450 |
| m_Egr-4 | 5′-GTATCCTGGAGGCGACTTCTT-3′ | 5′-CCTCTACTCCCCAGATCTGAGTT-3′ | 314 |
| Ephrin B2 | 5′-GTTGATAAAGACCAAGCAGACAGAT-3′ | 5′-GATGATGATGACGATGAAGATGAT-3′ | 489 |
| Fibronectin | 5′-GTCTATTCGCCATCAGTAGAAGGTA-3′ | 5′-CCAGGACAGTAGAATCAGTTTCATT-3′ | 514 |
| GAPDH | 5′-AGAACATCATCCCTGCCTCTACTG-3′ | 5′-TGTCGCTGTTGAAGTCAGAGGAGA-3′ | 258 |
| m_GFAP | 5′-AGGAGATCCAGTTCTTAAGGAAGAT-3′ | 5′-GCTTAACGTTGAGTAGATCCTGGTA-3′ | 486 |
| Laminin α1 | 5′-AGAGTGAGACAGGAACAAGAAGTAG-3′ | 5′-TAGCCAGAAGTACACACATCACAAT-3′ | 475 |
| Laminin α2 | 5′-GACCAGATGATTAAAGAACTGAGGA-3′ | 5′-CTCAGACATAGGTGGCAATTTAGTT-3′ | 441 |
| Laminin β1 | 5′-TGATTCTCGATATTCTGACATTGAA-3′ | 5′-CACGTACATCGTTCACAGAAATTAG-3′ | 630 |
| Phosphacan | 5′-AAAGGGAAGTTAAGAGCTTTATCCA-3′ | 5′-GAATCTCTTCCTTTCCAGTGTATGA-3′ | 403 |
| m_Phosphacan
|
5′-CATATACTGGAAAGGAAGAGATCCA-3′
|
5′-GTTCCTTTTTCCTTATTTGGTTTGT-3′
|
480
|
| T7 promoter-containing human EGR-1 PCR primers for siRNA preparation*
| |||
| EGR-1
|
5′-taatacgactcactatagggGGTCAGTGGCCTAGTGAGCATG-3′
|
5′-taatacgactcactataggggTCTGCTTTCTTGTCCTTCTGCCG-3′
|
559
|
| Primers used for mouse Egr-1 full length cloning†
| |||
| m_Egr1
|
5′-ggaattcCGCTGGTCCGGGATGGCAGCGGCC-3′
|
5′-gggatcccGCTTTCTTTTATTCCCTTTAGCAAAT-3′
|
1739
|
| OGNs used in the electrophoresis mobility shift assays‡
| |||
| Phos-1 | 5′-CTGCGCCCCCGCCCCCTCCAG-3′ | 5′-CTGGAGGGGGCGGGGGCGCAG-3′ | |
| GCE | 5′-GATCTCTCTCCTCCCCCGCGCCCCGGGG-3′ | 5′-CCCCGGGGCGCGGGGGAGGAGAGAGATC-3′ | |
| mGCE | 5′-GATCTCTCTCCTATACCGCGCCCCGGGG-3′ | 5′-CCCCGGGGCGCGGTATAGGAGAGAGATC-3′ | |
| OCT-1
|
5′-TGTCGAATGCAAATCACTAGAA-3′
|
5′-TTCTAGTGATTTGCATTCGACA-3′
|
|
| Primers used for human phosphacan promoter constructs§
| |||
| PTPRZ2_402 | 5′-CTGCGCCCCCGCCCCCTCCAG-3′ | 5′-CACTCTGAGAAGCAGAGGAGCCGC-3′ | |
| PTPRZ2_402mut | 5′-CTGCGCATATGCCCCCTCCAG-3′ | Same as above | |
| PTPRZ2_390
|
5′-CCCCTCCAGGAGCCGCGGCGC-3′
|
Same as above
|
|
| Primers used in the ChIP analysis
| |||
| Egr-1 site | 5′-GATTGTCGGTGTGTGAATTG-3′ | 5′-CTGTGCGCGCCGCGGCTCCTG-3′ | 149 |
| Distal 4.5 kb | 5′-CCTCCTACTTGTTTTATGCCTGATA-3′ | 5′-TTAAAAAGCAGTTCATTCCTACCTG-3′ | 109 |
*
T7 recognition sequences are underlined and in italics.
†
Sequences for the restriction enzymes EcoRI and Bam HI, with an extra g added to improve digestion efficiency, are underlined and in italics.
‡
Mutated nucleotides appear in bold and italics. The Egr-1 consensus site is underlined.
§
The Egr-1 consensus site is underlined. Mutated nucleotides appear in bold and italics.