The 102 sensors are 4.7×6.0cm each, and arranged in a large 1.0×0.5m field, and four more are used for quality checks.
The short (and provisional) discourse about quality factors for participatory (futures) research mentioned above can be summarised as follows: There is no set of rules that can be used for quality checking across all manifestations of research.
For FPKM value generation, cufflinks (version 2.1.1) was used for each transcript in each condition (three replicates for ESC and NPC) with default parameters; CummeRbund was used for quality checks and data access (Trapnell et al., 2013).
Each ligation reaction contained 4.9 µl of the RNA from the previous step (the remaining 0.3 µl was used for quality checks by CE), as well as 1× T4 RNA ligase buffer (NEB), 15% PEG 8000, 4 5 pmol ssDNA adapter, and 200 U T4 RNA ligase 2 truncated, K227Q or KQ mutant (NEB), in a 10 µl reaction volume.
Each microarray contains approximately 34,000 features that include a set of about 1,000 features that were used for quality control checks for IVT labeling, RT labeling, hybridization, dynamic range of chemiluminescent detection, spatial calibration, cross-talk and assay background.
BES quality scores were used for SNP quality checks in the AGSNP pipeline [ 25].
The dataset included 101 replicates and 773 sire-son pairs, used for downstream quality checking of the data produced.
RNA was eluted in 100 µl elution buffer, quantitated using Nanodrop ND-10000) and processed for quality check in Agilent bioanalyzer (Agilent, U.S.A).
Microarray analyses were performed using Affymetrix GeneChip® Operating Software GCOSS) for quality check, RMA-Express 0.3 for normalization and in-house statistical software for further testing (Nalimov test, ANOVA, t tests) and descriptive statistic (details provided in the Additional file 1: Table S8).
