Expression | Fold-change | P0 vestibule | Gradient (high to low) | Published HC gene | ChIP-seq | Atoh1 direct targets | Expression in Atoh1-CKO | |
---|---|---|---|---|---|---|---|---|
Anxa4 | 58650.61 | 74.378 | HC | Base to apex | No | Intestine | Yes | Decreased |
Atoh1 | 19042.08 | 474.258 | HC | Apex to base | Yes | Cerebellum, intestine | Yes | Decreased |
Calb2 | 9535.022 | 12.638 | HC | Not observed | Yes | Cerebellum | ND | ND |
Casz1 | 9969.698 | 85.483 | HC | Not observed | No | Cerebellum, intestine | ND | ND |
Chrna10 | 25097.05 | 503.115 | HC | Base to apex | Yes | Intestine | Yes | ND |
Chrna9 | 12030.11 | 691.694 | HC | Not observed | Yes | None | ND | ND |
Eps8l2 | 15530.19 | 64.052 | HC | Base to apex | Yes | Intestine | ND | ND |
Grxcr2 | 8326.395 | 584.267 | HC | Not observed | Yes | None | ND | No change |
Kcnh6 | 12791.54 | 154.773 | HC | Not observed | No | Intestine | ND | ND |
Kif21b | 8369.936 | 11.176 | HC | Base to apex | No | Cerebellum, intestine | ND | ND |
Lhfpl5 | 32615.66 | 573.769 | HC | Not observed | Yes | Intestine | ND | ND |
Lhx3 | 14148.41 | 452.087 | HC | Not observed | Yes | Intestine | ND | Decreased |
Mfng | 10493.52 | 76.080 | HC | Not observed | No | Cerebellum, intestine | ND | Decreased |
Mgat5b | 22037.06 | 214.706 | HC | Not observed | No | Cerebellum, intestine | Yes | No change |
Mreg | 16063.03 | 139.686 | HC | Base to apex | No | Cerebellum, intestine | Yes | No change |
Mycl1 | 26009.33 | 41.131 | HC | Not observed | Yes | Cerebellum, intestine | ND | ND |
Myo3b | 10718.11 | 374.468 | HC | Base to apex | Yes | Cerebellum, intestine | ND | ND |
Naca | 10408.7 | 24.968 | ND | Base to apex | No | Cerebellum, intestine | ND | ND |
Pacsin1 | 4302.44 | 40.762 | HC | Base to apex | No | Cerebellum, intestine | ND | ND |
Pcp4 | 26486.48 | 259.873 | HC | Base to apex | Yes | Cerebellum | Yes | No change |
Ptgir | 4722.92 | 133.553 | No | Base to apex | No | None | ND | ND |
Ptprq | 32675.67 | 331.022 | HC | Base to apex | Yes | None | ND | No change |
Rab11fip1 | 3025.383 | 89.836 | HC | Not observed | No | Intestine | ND | ND |
Rasd2 | 127825.8 | 507.234 | HC | Not observed | No | Cerebellum, intestine | Yes | Decreased |
Rbm24 | 16001.61 | 229.243 | HC | Not observed | No | Intestine | Yes | Decreased |
Scn11a | 11604.04 | 797.871 | HC | Apex to base | Yes | Cerebellum | Yes | Decreased |
Sema5b | 32913.11 | 29.366 | ND | Base to apex | No | Cerebellum, intestine | ND | ND |
Slc6a11 | 13126.97 | 309.753 | HC | Not observed | No | Cerebellum, intestine | ND | No change |
Smpx | 11162.48 | 275.918 | HC | Not observed | Yes | Cerebellum | ND | ND |
Srrm4 | 8899.872 | 164.984 | HC | Apex to base | Yes | Cerebellum, intestine | Yes | Decreased |
Stard10 | 30766.48 | 25.747 | HC | Not observed | No | Intestine | ND | ND |
Thsd7b | 28906.74 | 298.100 | HC | Not observed | No | Intestine | ND | No change |
Ttc21a | 16745.86 | 329.525 | HC | Not observed | No | Cerebellum, intestine | ND | ND |
Umodl1 | 10437.93 | 331.222 | HC | Not observed | No | Cerebellum, intestine | ND | ND |
Summary of genes whose specific expression in hair cells was validated by in situ hybridization. Gene name, expression level (RPKM), and fold-change over GFP− cells are indicated, together with expression pattern in the cochlea or vestibular system. If a transcript showed a gradient of expression in the cochlea, this is indicated. The table also lists whether each gene was identified as an Atoh1 target by ChIP-seq in either the cerebellum (Klisch et al., 2011) or small intestine (Kim et al., 2014), as well as whether the gene was shown to be a direct target of Atoh1 in the cochlea by ChIP-PCR (Fig. 5). Finally, the expression of direct Atoh1 target genes was measured in vivo 24 h after deletion of Atoh1 (Fig. 5).
HC, Hair cell; IHC, inner hair cell; ND, not determined.