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1420, 778, 13860, 352, 623, 3685, 1756, 940, 10861, 1866, 4219, 572, 387, 1391, 762, 789, 1092, 689, 745, 1424, 466, 1535, 315, 3340, 681, 2516, 18868, 1178, 572, 1176, 6430, 263, 438, 375, 1830, 1861, 1413, 2069, 15170, 1437, 381, 825, 10232, 1491, 439, 4018, 1091, 671, 2383, 2300, 2496, 22946, 1787, 3545, 4728, 3135, 668, 2257, 2206, 964, 1280, 1739]}}}], "discrepancies": [{"item": "Overall benchmarking rank (Fig. 6)", "paper": "Fig. 6 order: Quartz-seq2 (1) > Chromium V2 (2) > Smart-seq2 (3) > CEL-seq2 (4) > C1HT-medium (5) > C1HT-small (6) > ddSEQ (7) > Chromium-sn (8) > Drop-seq (9) > inDrop (10) > ICELL8 (11) > MARS-seq (12) > gmcSCRB-seq (13); harmonic mean of 6 metrics", "replication": "Gene medians, top5/bottom3: C1HT_medium (4630/27836) > C1HT_small (3682/19451) > QUARTZseq2 (3616/9298) > 10X_8x10K_25K (2319/3044) > SMARTseq2 (2116/54192) > ... > inDrop (596/908) > Dropseq (568/991) > MARSseq (531/845)", "note": "Top tier agrees (plate-based + Smart-seq2 lead). Composite here still ranks Smart-seq2 #1 on non-UMI read depth (artefact); 10X_8x10K_25K sinks on shallow depth + low stability (0.58). Paper depth-equalises to 20K reads/cell."}, {"item": "Read-depth equalisation", "paper": "20,000 reads/cell (lowest first quartile) + stepwise 25/50/75% via zUMIs; cells below threshold omitted", "replication": "Not performed; equal cell numbers only (1451/protocol)", "note": "Paper Fig. 2d-f library complexity is depth-controlled; our medians conflate depth with capture efficiency. Smart-seq2 read counts are not UMI-comparable."}, {"item": "Mitochondrial QC", "paper": "FACS viability sorting + QC on mapped counts with gene symbols", "replication": "median_mito_pct = 0.0 for all 15 protocols", "note": "Artefact: GEO matrices use ENSEMBL IDs (ENSG...), so MT-/MT. prefix match finds nothing. Mito filter effectively disabled; min_genes>=200 is the only QC."}, {"item": "Clustering accuracy / ASW (Fig. 4b)", "paper": "Seurat graph clustering (8 PCs, res 0.6) + matchSCore2 labels (p>=0.5); avg projection agreement 80% (Quartz-Seq2 92%, gmcSCRB-seq 58%)", "replication": "Louvain on 30 PCs/k=15/res=1.0; species-level labels (coverage 1.0: Human/Mouse/Doublet/Dog); ARI 0.00-0.25 by construction; subsample stability 0.64-0.94 (mean ARI, 5 repeats)", "note": "Species labels stand in for cell types, so ARI indexes species agreement, not cell-type accuracy (R24 high-precision/low-accuracy quadrant expected). Stability is a precision proxy."}, {"item": "Reference sample / cell numbers", "paper": "PBMC 60% / colon 30% / HEK293T 6% / NIH3T3 3% / MDCK 1%; Chromium reference 30,807 human + 19,749 mouse cells", "replication": "All 15 human SubSeries (QC-pass 15/15, equalised to 1451) + parallel 15-protocol mouse track (equalised to 1154)", "note": "Species doublets retained; no Chromium reference or matchSCore2 projection. Paper Fig. 6 ranks shown on mouse views are human-derived."}, {"item": "10X_V3 species-separated design (GSE141469)", "paper": "Joint human-mouse-dog mapping per protocol; species mix reported per protocol (Fig. 1)", "replication": "GSE141469 ships split matrices (human/mouse exp_mat); 10X_V3 composition is single-species by construction (Human 1.0 / Mouse 1.0)", "note": "Verified in data/metadata*.csv protocol x label crosstabs. 10X_V3 species shares (R25) and cross-species points (R29/R30) are not comparable with the other 14 jointly-mapped protocols."}], "similarity": {"genes_common": 24514, "qc_note": "means over cells with >=200 genes (mito gate skipped: ENSEMBL IDs)", "order": ["10X_2x5K_250K", "10X_8x10K_25K", "10X_V3", "C1HT_medium", "C1HT_small", "CELseq2", "Dropseq", "ICELL8", "MARSseq", "QUARTZseq2", "SMARTseq2", "SingleNuclei", "ddSEQ", "gmSCRBseq", "inDrop"], "correlation": [[1.0, 0.961, 0.663, 0.71, 0.71, 0.574, 0.713, 0.557, 0.73, 0.664, 0.561, 0.509, 0.732, 0.668, 0.701], [0.961, 1.0, 0.747, 0.77, 0.77, 0.638, 0.769, 0.639, 0.739, 0.726, 0.63, 0.542, 0.773, 0.696, 0.72], [0.663, 0.747, 1.0, 0.872, 0.875, 0.851, 0.863, 0.884, 0.718, 0.804, 0.877, 0.634, 0.781, 0.726, 0.765], [0.71, 0.77, 0.872, 1.0, 0.94, 0.842, 0.895, 0.841, 0.716, 0.858, 0.803, 0.613, 0.81, 0.691, 0.719], [0.71, 0.77, 0.875, 0.94, 1.0, 0.833, 0.859, 0.847, 0.73, 0.778, 0.813, 0.68, 0.819, 0.745, 0.76], [0.574, 0.638, 0.851, 0.842, 0.833, 1.0, 0.836, 0.79, 0.745, 0.782, 0.786, 0.713, 0.694, 0.64, 0.7], [0.713, 0.769, 0.863, 0.895, 0.859, 0.836, 1.0, 0.817, 0.719, 0.849, 0.802, 0.588, 0.769, 0.672, 0.716], [0.557, 0.639, 0.884, 0.841, 0.847, 0.79, 0.817, 1.0, 0.633, 0.731, 0.848, 0.607, 0.694, 0.68, 0.666], [0.73, 0.739, 0.718, 0.716, 0.73, 0.745, 0.719, 0.633, 1.0, 0.671, 0.634, 0.674, 0.697, 0.726, 0.76], [0.664, 0.726, 0.804, 0.858, 0.778, 0.782, 0.849, 0.731, 0.671, 1.0, 0.789, 0.477, 0.815, 0.602, 0.679], [0.561, 0.63, 0.877, 0.803, 0.813, 0.786, 0.802, 0.848, 0.634, 0.789, 1.0, 0.541, 0.757, 0.701, 0.722], [0.509, 0.542, 0.634, 0.613, 0.68, 0.713, 0.588, 0.607, 0.674, 0.477, 0.541, 1.0, 0.513, 0.601, 0.598], [0.732, 0.773, 0.781, 0.81, 0.819, 0.694, 0.769, 0.694, 0.697, 0.815, 0.757, 0.513, 1.0, 0.741, 0.775], [0.668, 0.696, 0.726, 0.691, 0.745, 0.64, 0.672, 0.68, 0.726, 0.602, 0.701, 0.601, 0.741, 1.0, 0.809], [0.701, 0.72, 0.765, 0.719, 0.76, 0.7, 0.716, 0.666, 0.76, 0.679, 0.722, 0.598, 0.775, 0.809, 1.0]], "cumulative": {"10X_2x5K_250K": [3016, 4534, 9346, 10875, 11789, 12040, 12334, 12578, 13004, 13071, 15101, 15243, 15386, 16036, 16211, 16268, 16291, 16417, 16530, 17229, 17282, 17890, 17928, 17961, 18118, 18157, 18626, 18635, 18668, 19223, 19317, 19495, 19552, 19575, 19592, 19632, 19639, 19680, 19688, 19985, 20143, 20393, 20425, 20446, 20465, 20483, 20701, 20881, 20923, 20942, 20990, 21021, 21033, 21047, 21086, 21249, 21300, 21332, 21441, 21447, 21470, 21694, 21744, 21759, 21774, 21801, 21828, 21852, 21870, 22099, 22116, 22211, 22230, 22295, 22375, 22381, 22537, 22560, 22573, 22727, 22757, 22890, 22912, 22994, 23064, 23077, 23346, 23503, 23511, 23536, 23577, 23591, 23598, 23796, 23967, 23979, 23986, 23991, 24009, 24033], "10X_8x10K_25K": [4785, 4918, 6235, 6783, 7193, 7407, 7554, 7919, 8119, 8253, 8374, 8658, 9205, 9273, 9461, 10329, 10748, 10913, 11129, 11750, 11823, 12201, 12252, 12315, 12337, 12413, 12817, 13062, 13122, 13282, 13671, 14100, 14183, 14210, 14263, 14356, 14376, 14406, 14448, 14772, 14802, 14930, 15001, 15266, 15320, 15605, 15672, 15712, 15771, 15805, 15833, 15858, 15874, 15886, 15902, 16139, 16172, 16247, 16272, 16290, 16370, 16431, 16445, 16470, 16497, 16509, 16535, 16604, 16629, 16645, 16659, 16673, 16691, 16715, 16781, 16810, 16828, 16834, 16854, 17090, 17150, 17165, 17175, 17333, 17342, 17436, 17495, 17573, 17583, 17600, 17604, 17619, 17635, 17698, 17773, 17799, 17805, 17820, 17842, 17897], "10X_V3": [1597, 2977, 4043, 5377, 6423, 6768, 9310, 9568, 10358, 10939, 11170, 11318, 12356, 12716, 12868, 13112, 13679, 13786, 13903, 13989, 14127, 14241, 14345, 14412, 14472, 14598, 14675, 14765, 14862, 14909, 14953, 15004, 15058, 15118, 15201, 15248, 15495, 15575, 15637, 15682, 15718, 15763, 15791, 15845, 15879, 15936, 16012, 16118, 16154, 16182, 16321, 16346, 16382, 16413, 16455, 16486, 16512, 16542, 16589, 16636, 16673, 16707, 16754, 16786, 16852, 16969, 17002, 17041, 17105, 17127, 17152, 17171, 17190, 17207, 17236, 17264, 17297, 17556, 17619, 17680, 17725, 17750, 18006, 18097, 18151, 18176, 18197, 18231, 18410, 18432, 18473, 18606, 18818, 18852, 18862, 18896, 18924, 18935, 18951, 19026], "C1HT_medium": [3551, 9527, 10922, 11775, 12945, 13823, 15801, 16518, 16753, 17535, 17918, 19910, 20517, 20718, 21135, 21246, 21330, 21482, 21981, 22567, 22654, 22766, 22839, 22904, 23079, 23166, 23230, 23305, 23579, 23642, 23703, 23750, 23875, 23925, 24019, 24063, 24188, 24254, 24321, 24376, 24435, 25163, 25212, 25364, 25501, 25532, 25662, 25720, 25776, 25793, 25971, 26208, 26378, 26520, 26549, 26648, 26680, 26739, 26824, 26909, 26989, 27139, 27209, 27278, 27299, 27558, 27579, 27668, 27680, 27707, 27735, 27869, 27889, 27967, 27989, 28021, 28052, 28075, 28128, 28161, 28186, 28219, 28254, 28266, 28421, 28440, 28457, 28687, 28714, 28827, 28872, 28932, 28943, 28951, 28976, 29025, 29045, 29055, 29063, 29084], "C1HT_small": [3248, 6912, 8276, 9897, 11417, 12021, 12742, 13096, 13696, 15036, 15735, 16160, 16386, 16688, 16908, 17159, 17461, 17877, 18300, 18541, 18759, 18933, 19100, 19528, 19683, 19783, 19870, 19986, 20188, 20284, 20396, 20529, 20660, 20735, 20894, 21002, 21094, 21251, 21317, 21459, 21530, 21630, 21708, 21785, 21863, 21985, 22062, 22179, 22231, 22288, 22350, 22456, 22508, 22616, 22684, 22751, 22804, 22859, 22913, 22992, 23035, 23081, 23229, 23324, 23399, 23820, 23860, 23907, 24056, 24086, 24136, 24170, 24222, 24271, 24312, 24372, 24430, 24480, 24516, 24550, 24586, 24620, 24657, 24688, 24723, 24746, 24807, 24865, 24913, 24963, 25260, 25291, 25330, 25353, 25398, 25443, 25483, 25511, 25532, 25569], "CELseq2": [2839, 5313, 5775, 7725, 8500, 8741, 9504, 9975, 10123, 12288, 12580, 13448, 13478, 13826, 14531, 14633, 15235, 16006, 16106, 16311, 16815, 16850, 17011, 17107, 17145, 17221, 17333, 17550, 17625, 17691, 17850, 17957, 17990, 18021, 18184, 18296, 18382, 18623, 18729, 18777, 19169, 19278, 19793, 20013, 20075, 20225, 20345, 20639, 20677, 20718, 20784, 21183, 21205, 21532, 21770, 21832, 21891, 22028, 22075, 22114, 22503, 22602, 22648, 22660, 22688, 22782, 23029, 23213, 23446, 23468, 23509, 23607, 23719, 23758, 23782, 23957, 23960, 23986, 23996, 24116, 24178, 24212, 24263, 24308, 24312, 24336, 24379, 24395, 24469, 24478, 24610, 24632, 24779, 24815, 25169, 25188, 25203, 25230, 25270, 25311], "Dropseq": [589, 1028, 2873, 3540, 4320, 4604, 4882, 5244, 5504, 5923, 6051, 6283, 6447, 6770, 7219, 7332, 7484, 7736, 7893, 7996, 8471, 8637, 8696, 8836, 8890, 9004, 9189, 9269, 9388, 10114, 10273, 10392, 10455, 10508, 10577, 11560, 11752, 11837, 11929, 12538, 12923, 12973, 13133, 13183, 13221, 13292, 13313, 13374, 13413, 13479, 13528, 13569, 13594, 13629, 13660, 13715, 13757, 13788, 13821, 13834, 13893, 14446, 14858, 14880, 14912, 14970, 15003, 15517, 15548, 15577, 15617, 15666, 15685, 15733, 15761, 15796, 15824, 15857, 15869, 15970, 15999, 16027, 16040, 16056, 16082, 16121, 16147, 16168, 16228, 16256, 16282, 16295, 16312, 16333, 16368, 16523, 16550, 16585, 16616, 16650], "ICELL8": [1724, 3097, 4186, 4940, 5542, 7059, 7512, 7721, 8529, 9083, 9445, 9611, 9752, 10212, 10419, 10681, 10993, 11078, 11232, 11742, 12079, 12312, 12424, 12986, 13095, 13392, 13520, 13581, 13798, 13903, 14472, 14520, 14927, 15031, 15222, 15452, 15726, 15758, 15798, 15959, 16056, 16196, 16316, 16356, 16426, 16563, 16598, 16636, 16751, 16899, 16954, 17049, 17111, 17288, 17427, 17487, 17545, 17623, 17687, 17750, 17847, 17931, 18070, 18106, 18127, 18299, 18373, 18405, 18440, 18531, 18568, 18654, 18674, 18716, 18764, 18856, 18918, 18930, 18972, 19019, 19052, 19095, 19129, 19156, 19166, 19305, 19380, 19405, 19423, 19609, 19633, 19688, 19726, 19798, 19846, 19876, 19919, 19976, 19989, 20027], "MARSseq": [341, 1137, 2201, 2882, 4105, 4941, 5646, 8590, 8857, 8973, 9592, 9799, 10702, 10821, 10931, 11049, 11190, 11310, 11393, 11870, 11937, 13680, 13817, 14072, 14310, 14610, 14650, 14703, 14873, 14963, 15008, 15307, 15381, 15464, 15623, 15754, 16049, 16337, 16603, 16656, 16737, 16838, 17015, 17585, 17659, 18489, 18590, 18625, 18665, 18786, 18797, 18820, 18838, 18858, 18971, 19020, 19106, 19244, 19301, 19392, 19411, 19557, 19605, 19617, 19749, 19766, 19795, 19814, 19839, 20634, 20651, 20805, 20822, 20835, 20906, 21004, 21149, 21182, 21192, 21236, 21294, 21412, 21443, 21446, 21462, 21468, 22114, 22155, 22215, 22286, 22321, 22392, 22436, 22466, 22501, 22532, 22547, 22554, 22758, 22820], "QUARTZseq2": [4857, 9032, 12097, 15245, 15440, 17072, 17612, 18054, 19052, 19393, 19430, 19746, 20085, 20212, 20655, 20864, 21149, 21772, 22047, 22102, 22149, 22245, 22564, 22607, 22768, 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