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Table 1 Studies identifying adult mammalian retina / RPE transcripts and details on gene data retrieval

From: The Retinome – Defining a reference transcriptome of the adult mammalian retina/retinal pigment epithelium

Reference Source / method a) Species b) Original dataset No. of genes retrieved c) (non-redundant) No. of genes identified in ≥ 2 studies
  In-silico projects     
[20] Retina, TIGR (ID: version 3.3) Hs 1,047 30 30
[19] Retina, TIGR (ID: version 3.3) Hs 1,315 11 11
[21] Retina, UniGene (ID: build 118) Hs 4,974 1,485 1,480
[22] Retina, UniGene (ID: build 113) Hs 6,190 46 45
[23] Retina, EST (dbEST) Hs 40,000 117 110
UniGene (Build 162) d) Retina Hs 3,560 1,612 1,211
UniGene (Build 162) d) RPE Hs 1,760 1,506 1,116
UniGene (Build 162) d) Retina & RPE Hs 11,976 9,178 9,178
  cDNA library sequencing     
[24] Fovea, conventional Hs 209 40 38
[25] Retina, conventional Hs 607 475 465
[37] Retina & RPE, SSH Hs 401 6 6
[30] Retina, subtracted Hs 137 49 48
[31] Retina, PC and subtracted Cf 173 66 65
[26] RPE, primary and amplified, conventional Hs 2,101 336 330
[38] RPE, SSH Bt 1,000 35 34
[27] and online e) Retina, PC Hs 2,701 2,096 2,059
[28] and online f) RPE, PC Hs 6,182 3,657 3,608
[29] Retina, PC (ID: MRA) Mm 1,793 421 412
[39] Retina, SSH Hs 1,080 310 301
[39] RPE, SSH Bt 2,350 343 329
  Microarray Analysis     
[32] Retina, Affymetrix (ID: Mu11K subB) Mm 6,540 67 67
[33] Retina, custom array Hs 10,034 530 508
  Serial Analysis of Gene Expression     
[34] Retina, adult Mm 54,009 4,233 3,974
[35] Retina (ID: HMAC2) Hs 102,359 7,269 6,919
[35] Retina (ID: HPR1) Hs 59,661 5,689 5,512
[35] Retina (ID: HPR2) Hs 105,312 7,268 6,955
[35] RPE (ID: HRPE1) Hs 53,666 5,755 5,211
Total (with inter-study redundancy)     52,630 50,022
Total (without redundancy)     15,645 13,037
  1. a) TIGR: The Institute for Genomic Research; EST: expressed sequence tag; RPE: retinal pigment epithelium; SSH: suppression subtractive hybridization; PC: primary, conventional b) Hs: Homo sapiens; Mm: Mus musculus; Cf: Canis familiaris; Bt: Bos taurus c) Genes with LocusLink ID identified based on publically available information d) [67], For query terms see (see additional File 15 e) [68], March 2003 f) [69], March 2003