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Table 1 Primers for ISH probes and RT-PCR

From: Postnatal developmental dynamics of cell type specification genes in Brn3a/Pou4f1 Retinal Ganglion Cells

Gene

Forward Primer Sequence

Reverse Primer Sequence

Product Size, bp

Incubation (P0-P7), h

Incubation (P14-P22), h

For 3’-UTR probes

 Ankrd13b

TCCAAGGGCGGAGGCAGGT

ATCAGGGAAGGGAAGAGGAAG

821 + (26)

5

6

 Cdh4

AAGTCCCAGCACTGATGAAAAA

CACCACCCGAATTGTTTGC

501 + (26)

6

6

 Elfn1

CCTGCGCAAGAAGGTTCAGTT

CTTGCTTGCTTGCACCAGGC

367 + (26)

6

6

 Eml1

CACTGTGATTTCTGTTTTGTCTA

GCCAGCCTCCCAAAGGGAG

473 + (26)

6

3

 Fam19a4

AACTTTATGAACCTTGGAGAATG

TGAAATTGGAGGCAAGATGACT

498 + (26)

6

3

 Foxp2

CTGTGCTGTTAGTGTAAAGATGT

GTTGCTTTCTAGAGTGTCATAAC

503 + (26)

3

3

 Gabra1

GTTCTTTTAGTCGTATTCTGTTG

GAGCTTGCAAAATAGATTTGCC

900 + (26)

6

6

 Grm4

GCCACACAGGCCTTCCTTCC

CTTCGAAACACACTCAAGATTAG

433 + (26)

6

5

 Hpca

CCTCTCCCTCGTGTCTATCC

GAGCTGGGACAAGAAGTGTTC

443 + (26)

6

3

 Plppr3

CAGTGCCAGCTCCGACTCTT

TTGCCAGGCTTAGTCCTGGTA

469 + (26)

6

6

 Mapk10

GTCACAACGCACTCACGAAAG

ATCTGTATCTACATCCATCTGAC

364 + (26)

6

5

 Nptx1

GGGGCTGAGAGCTCACTTG

ACCACTTCGAGCCACGCTC

600 + (26)

6

5

 Nptx2

TCTCCGTCCCAGAGGCCAC

CAGTTCCCTCAGACGGAAAG

486 + (26)

6

6

 Ntrk1

ATCGAGTGTATCACGCAGGGC

TATGATGGATGCTGGCCATGAA

328 + (26)

6

5

 Pcdh20

GACGAGTTTCCTACTTCTTGGG

TTATCGTTGATGTCCAGAAGAAG

511 + (26)

6

9

 Pick1

ACCACTGTAGGACAGCGAAGG

TTATTCAATACAGGCCCAGCTTC

393 + (26)

6

9

 Pip5kl1

ACAAGGTGTGTCGAAGTCGAAG

TAAGGGTTGGGGTCAGGGTC

458 + (26)

6

6

 Pnkd

CTTCACCATCCTCTTCATCACT

GAAGGTGGAAGATAGACTAGCC

360 + (26)

6

6

 Rims1

CACCCTCCTCTGGAGTCCAG

TGTGTCTGCAGTTTATACCAATG

500 + (26)

2

3

 Tmem25

TGCCTGTCCCTGTTGTGACC

GTACAAAACGATGCAGAGCTAC

687 + (26)

6

6

 Tmem91

CAACAAGGCTTGGGCCAAGG

GGGTATCTTTAATTTCTCACATTG

348 + (26)

6

5

 Tshz2

GCAGAAAGAAAGGGAAATATGTG

CATCACCTATTTGTTCTCTTCG

418 + (26)

6

6

 Tusc5

CTGGAGATCTCCGAACCTACAT

ATGGAGGATTTCCGTATGGCC

492 + (26)

6

5

 Pou4f1 (control)

TGTGTAGAAGATCCCCTTTGG

GCACAGAAATGGTTCTGATG

519 + (26)

3

3

For transcript-specific probes

 Clcc1 (pr.1 + pr.9) ^

CACAGCTGCGGGCCGAGC

CTGAGATTTCCTCATCGTTCCT

208 + (26)

  

 Clcc1 (pr.2 + pr.9)

AGTCCGCTCGGGACTCCAG

CTGAGATTTCCTCATCGTTCCT

181/252 + (26)

7

7

 Clcc1 (pr.3 + pr.9) ^

TGTTTGAGGTAGGCGGCTCG

CTGAGATTTCCTCATCGTTCCT

220 + (26)

  

 Clcc1 (pr.4 + pr.9) ^

TCGGCGTCTTCCGCGGCC

CTGAGATTTCCTCATCGTTCCT

203 + (26)

  

 Clcc1 (pr.5 + pr.9) ^

TCCCTCTGAAAGAGCAGGCAG

CTGAGATTTCCTCATCGTTCCT

172 + (26)

  

 Clcc1 (pr.6 + pr.9) ^*

TGAGTGGGCGCTCTTCGGTG

CTGAGATTTCCTCATCGTTCCT

293 + (26)

  

 Clcc1 (pr.7 + pr.9) ^

CGTTTCCAGGATACACCGAGA

CTGAGATTTCCTCATCGTTCCT

300 + (26)

  

 Clcc1 (pr.2 + pr.8) ^*

AGTCCGCTCGGGACTCCAG

CGGGTTAAGGGAAGTCAAATTC

199/270 + (26)

  

 Clcc1(pr.7 + pr.8) ^^

CGTTTCCAGGATACACCGAGA

CGGGTTAAGGGAAGTCAAATTC

159 + (26)

4

3

 Clcc1(pr.10 + pr.11)^

GTGAGGTCTGGAACATCAGAG

CATAAACACATTATATGGATCTA

432 + (26)

  

 Pnkd (pr.1 + pr.2)

TGGGACCCGAACATGGCGG

GGCTAGCCCCACGGCTTTC

246 (+  26)

2

3

 Pnkd (pr.3 + pr.4) *

TGTGGTATCCTCTTCTTCGTC

CTCCTTCCACGGTGTGGAAG

289 + (26)

2

3

 Pnkd (pr.5 + pr.6)

CCCAGCATGGCTTGGCAGG

CCGATTCGGAAGAGCAGCCG

167 (+  26)

2

3

 Pnkd (pr.5 + pr.7) ^

CCCAGCATGGCTTGGCAGG

ATTGAAGAGGCGGGGCTGAG

282 (+  26)

  
  1. Left column represents gene name, or gene name together with primer combination for transcript-specific probes. Second and third columns show primer sequences, fourth column shows product length, fifth and sixth columns represent ISH probe incubation times for P0-P7 and P14-P22 retinas. Some of the primer combinations could give rise to two different DNA fragments depending on splice variants. ^ - primer combination used for RT-PCR not ISH. ^^ - primer combination used for ISH not RT-PCR. * - primer combination gave negative result in RT-PCR. Primer combinations pr.3 + pr.8, pr.4 + pr.8, pr.6 + pr.8 for Clcc1 not shown in this table also gave negative results (for predicted fragment sizes see Table 2). Numbers in parenthesis refer to T3 promoter extension, as required for ISH probe generation