Do reprogramming papers say what the cells were grown in, on, and whether the dish was shaken?

Answer

For vessel and surface the answer is essentially yes; for agitation it is essentially no. Surface (feeder cells or a coating matrix) is stated in every paper the census counted — 9 of 9 [b4769b05], 9 of 9 [ff299867], 8 of 8 [c0cc9bb7], 8 of 8 [530765c8], 6 of 6 [6d4e8727], and in all six additional out-of-list papers examined [086eea09]. The vessel or format is stated almost as reliably, at 8 of 9 [ff299867], while dish or plate size specifically is named in only four of six human papers in one pass [6d4e8727]. Agitation is the outlier: 1 of 9 papers [ff299867], 1 of 8 [c0cc9bb7], 0 of 6 [086eea09], 0.0 of 2 [781d32f0], and only one paper of nine states all three details together [ff299867]. That single paper is Lam 2022, where Laminin-521-coated microcarriers in 6-well ULA plates were shaken at 100-110 rpm and reached TRA-1-60+ colony efficiency of 0.97 ± 0.1% in RepMC versus 0.02 ± 0.01% in RepMNL (47.6 ± 7.5-fold; mean ± SD, n=3, p<0.0001) [f571bb13]. Papers that do report conditions in detail show how much the omission costs: Schlaeger 2015 states dishes and surfaces for each method but never states agitation, and its Sendai arm reached 0.077% efficiency on feeder cells in 10-cm gelatin dishes [56b6ff4f]; Kogut et al. specify Geltrex-coated 6-well format dishes and Geltrex-coated 48-well plates with no agitation stated anywhere, alongside an FN2 efficiency of 779.2 ± 26.23% (TRA-1-60-positive colonies divided by 500 initially plated cells; mean ± SD, n=3) [72065216].

Summary

A reader should take away that the physical culture surface is treated as a reportable method detail by this literature and the vessel almost as consistently, but whether the culture was static or agitated is not — it appears in a single paper out of every denominator the census has used, and that paper is the one whose entire result is about agitation. The important disagreement in the corpus is not about that conclusion but about the denominator. Independent passes report 3 [189d8daa], 6 [bb5c5185], 7 [deef291b], 8 [c0cc9bb7], and 9 [ff299867] papers examined, plus 2 [781d32f0] and 6 [086eea09] papers outside the starting list; the counts are not additive, they reflect different reading depth (full text versus retrieved passages) and partly different paper sets, and the largest totals were explicitly withdrawn after audit [f571bb13]. A second, quieter caveat: where a paper compares methods, the surface is held explicitly equal in only 3 of 9 [b4769b05], and Schlaeger and Kuebler used different surfaces in different arms [530765c8], so some reported efficiency gaps between methods are confounded with surface and format rather than being clean comparisons [56b6ff4f].

Evidence

• Census pass, N=9 (Xu 2013 excluded: mouse cells) — vessel/format and surface/feeder each stated in all 9 papers; agitation/motion stated in only 1 of 9 (Lam 2022); where compared arms exist, surface is held explicitly equal in only 3 of 9 (Trevisan 2017, Okumura 2019, Manzini 2015). b4769b05
• Nine-paper count — all nine state the surface, eight state the vessel, only one (Lam 2022, agitated microcarriers at 100-110 rpm) states agitation status; the other eight never say static or agitated; only one of nine states all three. ff299867
• Census dated 2026-09-19, 9 papers full text — all 9 state vessel/format and surface; only 1 (Lam 2022, microcarrier arm at 100-110 rpm) states static versus agitated; Schlaeger 2015 does not hold vessel and surface constant across arms. 0f7047fd
• Eight scored human papers after auditor feedback — Warren 2010 newly scored: 6-well plates or 10-cm dishes, gamma-irradiated human neonatal fibroblast feeders, no agitation stated; all 8 name a vessel and a feeder or coating, only Lam 2022 says anything about agitation (1 of 8); Simara 2014 available only as an abstract and not scored. c0cc9bb7
• Eight human papers, full-text passages — all 8 gave a vessel or format and a surface; only one (Lam 2022) described shaking (100-110 rpm) versus static culture; in Lam 2022 both arms sat on laminin-521, so they differ in format and agitation but not surface; Schlaeger and Kuebler used different surfaces in different arms; search used top-ranked passages rather than line-by-line reading. 530765c8
• Seven of ten seed papers, methods passages — six use human cells; all six state feeders or a coating (MEFs, Matrigel, laminin 521); four name the dish or plate size; none says in the retrieved text whether the culture was static or shaken; Lam 2022, Okumura 2019 and Simara 2014 not read. 6d4e8727
• Ten papers, seven read — all human-cell studies use flat plates or dishes on feeder cells or a coating; only Lam 2022 states agitation, with a microcarrier arm shaken at 100-110 rpm on Laminin521-coated microcarriers and a static monolayer arm on a laminin substrate; elsewhere shaking is not mentioned in the passages retrieved, so "not stated" rather than proven absent. deef291b
• Six of ten seed papers, full text — all six name a plate or dish and a feeder, coating or matrix; only Lam 2022 says anything about motion, reporting that agitated cultures outperform non-agitated ones; four seed papers not examined. bb5c5185
• Three of ten listed papers — all three name a vessel and a surface (feeder, Matrigel or laminin coating); only Lam 2022 addresses agitation, contrasting shaken (100-110 rpm) with non-shaken culture and reporting much lower efficiency without agitation. 189d8daa
• Two out-of-list papers, Goh 2013 and Ono 2012 — both name the vessel format and the surface; neither says whether the culture was static or agitated, nor that these conditions were identical across arms; 0.0 papers stating static or agitated culture. 781d32f0
• Six further out-of-list papers (Fusaki 2009, MacArthur 2012, Lin 2012, Zhang 2011, Timilsina 2023, Vashistha 2026) — all six name the vessel format and the surface, none states whether the culture was static or agitated. 086eea09
• Kogut et al., feeder-free RNA protocol — Geltrex-coated 6-well format dishes plus a separate single-cell assay on Geltrex-coated 48-well plates; agitation not stated anywhere in the text; FN2 efficiency 779.2 ± 26.23% (TRA-1-60-positive colonies divided by 500 initially plated cells; mean ± SD, n=3). 72065216
• Schlaeger 2015, Sendai vs episomal vs mRNA — states the dishes and the feeder or Matrigel surface for each method but never says whether cultures were agitated; Sendai virus reached 0.077% efficiency on feeder cells in 10-cm gelatin dishes; because methods grew on different surfaces the efficiencies are not a clean like-for-like comparison. 56b6ff4f
• Lam et al. 2022, single verified row — RepMC uses 6-well ULA plates with Laminin-521-coated microcarriers under 100-110 rpm agitation; TRA-1-60+ colony efficiency 0.02 ± 0.01% in RepMNL versus 0.97 ± 0.1% in RepMC (47.6 ± 7.5-fold; mean ± SD, n=3, p<0.0001), counted on day 14 per initial cell seeding; the unsupported 14-paper totals are withdrawn. f571bb13

Methodology

Each pass was treated as its own row of the census and never merged into a pooled total, because the denominators overlap without being identical: passes read 3, 6, 7, 8 or 9 papers, some from the starting list and some from outside it, and some read full text while others relied on top-ranked retrieved passages, so adding them would double-count papers and inflate the apparent coverage. I also respecte