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Table 3 primers used in this paper

From: Acute stress alters transcript expression pattern and reduces processing of proBDNF to mature BDNF in Dicentrarchus labrax

 

NAME

SEQUENCE 5'-3'

Tm°C

Notes

Genome Walking

1beta_SP1

CCACTGAGTCCAACCCTTCCAGCAATGC

72.2

3

 

1beta_SP2

ACCATTTTCCCCTACGCTGTCCTGGAGATAG

70.2

3

 

1beta_SP3

ACTTCTGCTGTGCTCAGTAGATCGCCCACC

71.9

3

 

1beta_SP4

GGCAAATATCAACAAGCCCGGGTTGTCAG

72.0

3

 

1beta_SP5

GGCAATCCAAGTTTGTGGGGGTACTAGTTC

68.3

3

 

1beta_SP6_A

GAGTGTTAACTCCCTCTTTGGCGAGGGG

69.7

3

 

1beta_SP6_B

GGCCTATTACGCATACGCACAAACTGGTC

69.0

3

 

AP1

GTAATACGACTCACTATAGGGC

59.0

4

 

AP2

ACTATAGGGCACAGCGTGGT

71.0

4

Genomic PCR

Dl_ex1beta_fw

CCAAGTGGTGGGCGATC

57.6

2

 

Dl_ex1c_fw

CCATGCAATTTCCACCATC

54.5

2

 

Dl_ex1a_fw

GTTAACTTTGGGAAATGCAAG

54.0

2

 

Dl_P1_ant_BDNF

CCATAGTAACGAACAGGATG

55.3

2

 

Dl_P2_ant_BDNF

GTCATCACTCTTCTAACCTGTTG

58.9

2

 

Dl_ex1a_rev

CACTTGCATTTCCCAAAGTTAAC

54.0

2

 

Dl_ex1c_rev

GATGGTGGAAATTGCATGG

54.5

2

 

Int1c/2_FW

CCAGACAGTTTCTGTATTGTTGTTTTGGAGGGG

70.2

3

 

Int1c/2_REV

TCCAGCCATGTGAGGATCAATTGTGAACGG

73.6

3

 

Int1c/2_up

GTATTTTCTTAATTGCACACAGCGTGGGTGGG

71.4

3

 

Int1c/2_low

CATTCTTAATTGGTATCTGGGGCCGTGGC

71.0

3

 

Int1c/2_FWnew

CTCTAGGTGCGTTGTCATGCACAAAGGC

69.8

3

 

Int1c/2_REVnew

AGGGGTAATATTGCAGTAGCAGGGGGTGG

70.0

3

 

Int1a/1c_FW

ATGCTCCCAATATGGGACCTTAAGACGCTGC

72.2

3

 

Int1a/1c_FWnew

GTAATCGTTGCGTTGTGCTTAATCATGCTCC

66.8

3

 

Int1a/1c_FW1

GGTCTGCTGCATTCATGTTTTGTCTTGATG

68.7

3

 

Int1a/1c_FW2

GCCCTACTCTTTACCCCCCCCACCC

70.2

3

 

1crev_SP1

TCTCCCGACAAGCTTCAGGATATCTCTTCAGC

70.8

3

 

Int1a/1c_REV_1

TTTTGCGTAACIGCGCGTCTCCACCAIGTC

74.5

3

 

Int1a/1c_REV_2

CAAACTCCTGGATATGAGCTTAAAGGAGGC

66.4

3

 

Int1a/1c_REV_3

CGTTTGGCATGTAGCAGTATGGGAGTGG

69.3

3

 

Int1a/1c_REV_4

CCTTTCAAGGCTTCTCTTGCCAAATGC

68.2

3

 

Int1a/1c_REV_5

CATCCTGCCAGCATGTGCAACTGC

69.6

3

 

Int1a/1c_REV_6

CCTGACTCACTTTTAGCCTATCTGACATGCAGG

69.3

3

 

Int1a/1c_REV_7

CACACACACACACACACACACACACTGTG

68.3

3

 

Int1beta_FW

GACCAGTTTGTGCGTATGCGTAATAGGCC

69.0

3

3'-RACE

SP1FW_3'

GGCTGCAGAGGAATAGACAAGCGGCAT

70.4

3

 

SP2FW_3'

CCAATGCAGGACAACCCAGTCCTACGT

69.3

3

 

BDNF_3'race

GACCATTAAGAGGGGCAGATAG

60.3

3

 

AP

GGCCACGCGTCGACTAGTACTTTTTTTTTTTTTTTTT

71.1

4

 

UAP

CUACUACUACUAGGCCACGCGTCGACTAGTAC

64.3

4

5'-RACE

RACE_BDNF_GSP1

CTTGGTTGCTGATCATC

50.4

3

 

RACE_BDNF_GSP2

CTGTGAGTGAGGGCAGTTC

58.8

3

 

RACE_BDNF_GSP3

CGAACAGGATGGTCATCACTC

59.8

3

 

AAP

GGCCACGCGTCGACTAGTACGGGIIGGGIIGGGIIG

> 75.0

4

 

AUAP

GGCCACGCGTCGACTAGTAC

66

4

RT-PCR

Dl_BDNF_up

ATGACCATCCTGTTCGTTAC

55.3

2

 

Dl_BDNF_down

CTATCTGCCCCTCTTAATG

54.5

2

 

1beta_FW_nested

GCGAGGGTGTTACGTATATCTG

58.7

3

 

1beta_Rev_new

CCACTCACTCCAACAGATGC

59.3

3

 

1a_FW_new

GCTTATTCTGAGGGAGCCTG

59.0

3

 

1a_Rev_new

CCCAAAGTTAACGCAGTGTG

59.2

3

 

1bFW

CTCAGCTCTGCAGAGTTGGGGT

61.8

3

 

1c_FW_new

CGTTTCACCATGCGACAAC

61.1

3

 

1c_Rev_new

GCCCAGTCGTAAAACAGACC

59.6

3

 

1dFW

GTCCTGATGGAAACAGGAAATCAC

63.1

3

 

1dRev

CACAGATGACGTCTCTTCCAGGT

62.9

3

 

Ex2_FW_new

CTTCAGTTGCATGAGAGCTGC

61.3

3

 

Ex2_Rev_new

ACCCTCATGCACATATTAGCG

60.0

3

 

Dl_BDNFreal_low

TTGCTTCAGTTGGCCATTGG

57.3

3

 

Dl_Act_FW_RT

GGTATTGTCATGGACTCCGGTGAT

61.9

1

 

Dl_Act_Right

TTAGAAGCATTTGCGGTGGA

58.0

1

 

D.l._GAPDH_FW

GAGGGTGACAAGCTGGTCGT

58.8

1

 

D.l._GAPDH_Rev

CAAAGATGGAGGAGTGAGTGTCAC

58.8

1

Universal Primers

T7

TAATACGACTCACTATAGGG

53.2

 
 

SP6

CATTTAGGTGACACTATAG

50.2

 
  1. 1 - primers deduced on sequences available in public databases (Actin: AY148350; GAPDH: AY863148). 2 - primers deduced on ortologue sequences (BDNF: Danio rerio AL935207 clone CH211-251J8; Fugu rubripes http://www.fugu-sg.org/ scaffold_1; Paralichthys olivaceus AY074888). 3 - primers deduced on obtained sequences. 4 - primers included in the kits used during the experiments.