Table 2. All the heatmap clusters which include outlier genes are listed with their expression description, their classification (if one had been assigned) and the outlier genes separated by whether they were from hearing difficulty outlier lists or normal hearing outlier lists. Thirteen genes are present in both a hearing difficulty outlier list and a normal hearing outlier list. Known deafness genes are in bold. RM: Reissner's membrane; OC: Organ of Corti; LW: lateral wall; SGN: spiral ganglion neurons; SC: supporting cell; HC: hair cells; OHC: outer hair cells; IHC: inner hair cells; IPhC: inner phalangeal cells; DC: Deiters' cells; PC: pillar cells

Cluster 1A

Middle in RM and OC, mid-low in LW, low in SGN and SC

Cells of the cochlear duct (Myh14)

Mrpl38, Trp53i13, Dnpep, Atp6v0a2, Arhgap17, Myh14, Tgfbr1, Itgb1bp1

Krt10, Yy1, Prkra, Txndc16, Nsrp1, Sap30bp, Gpr180, Maz, Rae1, Zfpl1, Itgb1bp1, Dpp7, Proser2

Cluster 1B

High in HC, mid-high in rest of OC, middle in RM, mid-low in LW, low in SC

Organ of Corti and fibrocytes

Ddx52, Dxo, Acp6, Rrp9, Itsn2, Dlg5, Ptpn13

Lmf2, Gas8, Svil, Mus81

Cluster 1C

High in OHC, middle in rest of OC and RM, mid-low in LW, low in SC and SGN

Outer hair cells

Snapc3, Mink1

Mink1, Prdm2, 4932438A13Rik

Cluster 1D

High in OHC, mid-high in rest of OC, mid-low in LW and SC, low in RM and SGN

Hair cells (Synj2)

Ube3b, Synj2, Tacc2

Mpdz, Tacc2, Hyou1

Cluster 1E

Mid-high in HC, middle in rest of OC, middle in fibrocytes, mid-low in RM and SC, low in rest of LW and SGN

Hair cells

Madd

Ubr4, Peg3, Cadm1

Cluster 1F

Mid-high in OHC, middle in rest of OC, middle in RM, fibrocytes, Hensen cells and IPhC, mid-low in rest of SC and rest of LW, low in SGN

Outer hair cells

Brd4, Ubtf, Bri3bp, Sfxn5, Nav2

Srp68, Kdm5a, Nav2

Cluster 1G

Mid-high in OC and RM, mid-low in LW, SC, low in SGN

Organ of Corti and Reissner’s membrane

Kmt2c, Agrn, Htt

Gramd1a, Kdm1a, Agrn, Leng8

Cluster 1H

Mid-high in HC and RM, mid-low in rest of OC, LW, SC, low in SGN

Hair cells and Reissner’s membrane

Vwa8, Vps13b, Cgn

Atr, Sgip1

Cluster 1I

Low in SC, SGN and marginal cells, middle in OC, RM and rest of LW

Numa1, Pdlim5, Hnrnpa0, Pam

Dmxl1, Arid1b, Polg, Numa1, Tjp1, Etl4

Cluster 1J

Middle in OHC, RM and rest of LW, low in rest of OC, spindle/root cells, SC and SGN

Rin2

Cluster 1K

Mid-high in pillar cells, middle in rest of OC, fibrocytes and IPhC, low in rest of LW, rest of SC, SGN and RM

Pillar cells

Adamts2, Me3, Col11a1, Lamb2, Itpr2, Fzd9

Zfpm1

Cluster 1L

Middle in pillar cells and fibrocytes, mid-low in RM, OHC, basal cells, spindle and root cells, low in rest of OC, rest of LW, SC and SGN

Lama2

Hmcn1, Rgs3, Pgm5, Synm, Rcl1, Lama2

Cluster 1M

Mid-high in LW, middle in OC, mid-low in SC, low in SGN and RM

Stria vascularis (Kcnj10)

Slc12a2

Cluster 1N

Mid-high in OC, low in LW, SGN, SC and RM

Hair cells (Pcdh15)

Grwd1, Surf6, Tjap1, Tmprss9

Eif2b3, Grwd1, Nop9, Celsr1, Man2b2, Tcerg1, Cog4, Sema6d, Rgs11

Cluster 1O

High in HC, middle in PC, low in DC, SGN, RM, LW and SC

Hair cells (Atoh1, Pou4f3, Otof)

Fscn2, Chrna10, Lmod3

Lmod3

Cluster 1P

High in HC, low in rest of OC, SGN, RM, LW and SC

Hair cells (Myo7a, Ptprq)

Cdh23, Loxhd1

Osbp2

Cluster 1Q

High in HC, middle in DC, low in PC, SGN, RM, LW and SC

Hair cells (Tmc1)

Tmc1, Strip2

Tmprss7

Cluster 1R

High in OHC, mid-high in rest of OC, mid-low in SC, low in LW, RM and SGN

Organ of Corti

Rnf128, Otog, Dnaja4, Ush1c

Cluster 2A

Middle in OC and RM, mid-low in LW, low in SC and SGN

Atxn7, Noc2l, Nob1, Capn10, Cog1, Iqcb1, Elmo3, Slc9a8, Aldh4a1, Szt2, Dach1, Tcirg1, Pkp3, Chmp4c

Rfx7, Fggy, Cep295, Zfp142, Sec24d, Pld2, Lgr4, Dock6, Baz1a, Gli3, Sft2d3, Abca3, Slc39a3, Cnksr1

Cluster 2B

Middle in OC, mid-low in LW, low in RM, SC and SGN

Vps13a, Rbl2, Manea, Cep63

Diaph1, Vps13a, Ints1, Abcb8, Flna, Maml2, Nectin1, Klhdc10, Plec, Fam189b

Cluster 2C

Low in DC, middle in rest of OC, low in LW, SC, RM and SGN

Frmpd1, Hgh1, Myom1

Hectd4, Frmpd1, Tsr1

Cluster 2D

Middle in SGN and RM, mid-low in OC, low in SC and LW

Spiral ganglion neurons

Tango2, Prune2

Ercc6, Kif1a

Cluster 2E

Middle in HC, low in rest of OC, LW, SC, RM and SGN

Hair cells (Whrn)

Dll3, Ppp6r2, Fer1l6, Rimkla

Dll3, Pkhd1l1, Fam81b, Pdzd7, Adgrv1, Xirp2, Myo3a, Angpt1, Abca7, Obscn, Mn1, Dvl3, Pjvk, Ltbp1

Cluster 2F

High in OHC, middle in IHC, low in rest of OC, LW, SC, RM and SGN

Outer hair cells (Slc26a5)

Gpr152, Slc26a5

Cluster 2G

High in OHC, low in rest of OC, LW, SC, RM and SGN

Outer hair cells

Bmp3

Tub, Sec16b

Cluster 2H

Middle in fibrocytes, mid-low in rest of LW and SC, low in RM, SGN and OC

Fibrocytes

Mylk

Lamb1, Afap1l2, Fbln7, Wfdc1

Cluster 2I

Mid-high in IHC, middle in DC and PC, low in OHC, LW, SGN, SC and RM

Inner hair cells

Dmd, Piezo1

Cluster 2K

Mid-high in PC, middle in RM, fibrocytes and spindle/root cells, low in rest of OC, rest of LW, SGN and SC

Pillar cells

Thsd7a

Cluster 2L

Middle in RM and fibrocytes, mid-low in rest of LW, low in OC, SC and SGN

Pcolce, Ccdc141

Cluster 2M

High in RM, mid-high in spindle/root cells, low in rest of LW, SGN, SC and OC

Reissner’s membrane

Ap1s3, Atp13a5, Slc26a7

Frem1, Slc26a4

Cluster 3A

Middle in OC, RM, LW and SC, low in SGN

Cochlear epithelium (Sox10)

Eif5b, Tcn2, Sdf2l1, Auts2, Mpnd, Sipa1l1

Abhd14b, Zfhx3, Syne2, Nadk

Cluster 3B

High in OHC, mid-high in IHC, middle in rest of OC, RM, LW and SC, low in SGN

Hair cells (Myo6)

Nbeal1, Myo6

Brd2, Hspa4

Cluster 3C

High in PC, low in marginal cells, RM and SGN, middle in rest of OC, rest of LW and SC

Pillar cells

Txndc5, Irf2bpl

Ddrgk1

Cluster 3D

Low in marginal cells and SGN, middle in OC, RM, rest of LW and SC

Dguok, Fndc3a, Asap1

Kdm6b

Cluster 3E

Low in SGN, marginal and intermediate cells, high in PC, mid-high in rest of OC, fibrocytes and IPhC, middle in RM, rest of SC and rest of LW

Sensory epithelia (Six1)

Igfbp5

P3h4, Col11a2

Cluster 3F

High in OC, middle in RM, SC and spindle/root cells, low in rest of LW and SGN

Organ of Corti

Dpp4

Cluster 3G

High in OC, IPhC and spindle/root cells, middle in RM, rest of SC and fibrocytes, low in SGN and rest of LW

Organ of Corti, inner phalangeal and spindle/root cells

Gpx2

Cluster 3H

High in HC, mid-high in rest of OC, middle in SC, mid-low in LW and SGN, low in RM

Hair cells

Ciapin1, Kif21a

Nceh1, Ciapin1

Cluster 3I

Middle in DC, high in rest of OC, fibrocytes and spindle/root cells, middle in rest of LW and SC, mid-low in SGN, low in RM

Cells of the cochlear duct

Prdx5, Ndufv3

Srp14, Capns1

Cluster 4A

Middle in marginal cells, high in rest of LW, OC, RM and SC, low in SGN

Cells of the cochlear duct

Gjb2