|
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)
| | |
- 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
