Exact(4)
The purpose of this contig-filtering step was to remove potential contamination, which can be difficult to identify in de novo transcriptome assemblies that lack genomic context.
In brief, human seminiferous tubules were obtained from the testis tissues using the first enzymatic digestion and extensive washes using PBS to remove potential contamination of myoid cells.
Deconseq 0.4.2 was used to remove potential contamination using custom human, arthropod, bacterial, and protist databases (using all available genomic sequence for the latter two clades, as downloaded from National Center for Biotechnology Information [NCBI] on September 16, 2014).
To remove potential contamination of genomic DNA, total purified RNA was incubated with RQ1 (Promega) DNase at 37°C for 40 min and then inactivated at 65°C for 10 min.
Similar(56)
Cross-contamination check was also conducted on FPminer to remove potential contaminated clones.
The RNA was treated with RNase-free DNase I (Promega Italia, Milan, Italy) to remove potential DNA contamination.
RNA was treated with DNase I (Roche, South San Francisco, USA) (1 hr; 37°C) to remove potential DNA contamination.
Prior to germination, seeds were surface sterilized according to Groome et al. (2009) to remove potential fungal contamination and then stratified to improve germination rates.
To remove potential DNA contamination, 2 μg of total RNA was treated with DNase I (Invitrogen) and then reverse transcribed with Superscript II reverse transcriptase (Invitrogen).
After collection using the RNeasy mini kit (Qiagen; Mississauga, ON), total RNA was digested with DNase I to remove potential DNA contamination, and then reverse transcribed to cDNA using the Superscript II Reverse Transcriptase System (Invitrogen Burlingtonn, ON, Canada).
Commercially available calf thymus histones (Sigma, Deisenhofen, Germany) were passed through a high affinity endotoxin detoxi-gel (Thermo Fisher Scientific, Waltham, Massachusetts, USA) before use in all stimulation assays to remove potential endotoxin contamination.
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