# Photoreceptor scRNA-seq (GSE175929 / PMID:34462505): guca1a guca1b guca1c guca1d guca1e guca1g gnat2 gnat1

## Gene positions in the authors' GTF

- guca1a: feature ids ['LL0000011859']; locus ['chr4', 22343093, 22350976]
- guca1b: feature ids ['LL0000011860']; locus ['chr23', 19227296, 19230627]
- guca1c: feature ids ['LL0000011861']; locus ['chr15', 2884711, 2903475]
- guca1d: feature ids ['LL0000011862']; locus ['chr21', 22904396, 22910530]
- guca1e: feature ids ['LL0000011863']; locus ['chr22', 1092479, 1109547]
- guca1g: feature ids ['LL0000011864']; locus ['chr25', 14092871, 14096311]
- gnat2: feature ids ['LL0000011454']; locus ['chr8', 25225590, 25247284]
- gnat1: feature ids ['LL0000011453']; locus ['chr6', 42918933, 42930302]

matrix: 37375 features x 12833 barcodes
assignment: opsin UMI >= 5 and dominant opsin group >= 80% of opsin UMI; bipolar = no opsin UMI and >= 2 cabp5a+vsx1 UMI

## Fraction of cells with >= 1 UMI / mean CP10K

| gene | rod (n=1866) | UV cone (n=126) | blue cone (n=544) | green cone (n=526) | red cone (n=387) | bipolar (cabp5a/vsx1) (n=0) |
|---|---|---|---|---|---|---|
| guca1a | 0.61 / 4.8 | 0.17 / 0.2 | 0.13 / 0.2 | 0.15 / 0.1 | 0.14 / 0.1 | NA |
| guca1b | 0.84 / 15.9 | 0.26 / 0.5 | 0.22 / 0.5 | 0.22 / 0.2 | 0.22 / 0.2 | NA |
| guca1c | 0.99 / 28.5 | 1.00 / 57.0 | 1.00 / 56.6 | 1.00 / 73.3 | 1.00 / 75.3 | NA |
| guca1d | 0.38 / 1.9 | 0.80 / 3.5 | 0.88 / 5.1 | 0.98 / 6.8 | 0.95 / 6.8 | NA |
| guca1e | 0.08 / 0.3 | 0.68 / 2.5 | 0.48 / 0.8 | 0.36 / 0.3 | 0.19 / 0.1 | NA |
| guca1g | 0.02 / 0.1 | 0.04 / 0.0 | 0.13 / 0.1 | 0.23 / 0.2 | 0.19 / 0.1 | NA |
| gnat2 | 0.99 / 22.5 | 1.00 / 76.6 | 0.99 / 46.5 | 1.00 / 58.9 | 1.00 / 53.6 | NA |
| gnat1 | 0.99 / 93.4 | 0.63 / 1.4 | 0.66 / 1.6 | 0.67 / 0.8 | 0.63 / 0.7 | NA |

## Mean CP10K ratio rod / mean of cone types (ambient yardstick: gnat2, gnat1)

- guca1a: rod 4.81, cone mean 0.15, rod/cone = 31.64
- guca1b: rod 15.88, cone mean 0.32, rod/cone = 48.96
- guca1c: rod 28.48, cone mean 65.55, rod/cone = 0.43
- guca1d: rod 1.91, cone mean 5.56, rod/cone = 0.34
- guca1e: rod 0.28, cone mean 0.95, rod/cone = 0.29
- guca1g: rod 0.06, cone mean 0.11, rod/cone = 0.61
- gnat2: rod 22.51, cone mean 58.90, rod/cone = 0.38
- gnat1: rod 93.42, cone mean 1.12, rod/cone = 83.28