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Four libraries were constructed by using the SMART method (Clontech, Palo Alto, CA, USA) [ 22].
These rRNA and chloroplast genes could not be removed using the SMART method during the cDNA library construction and normalization process because they are not identical and cannot be removed and digested by duplex-specific nuclease.
The comparison between control and depleted libraries prepared using the SMART method revealed a greater bias, especially for the L. lactis sample (Additional file 2: Figures S8 and S9).
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To compile the remaining four libraries, because only small amounts of RNA could be prepared from the tissues or cell populations, we used the SMART method and pDNR-LIB vector (Clontech, Palo Alto, CA, USA); this method selectively clones cDNAs that are synthesized as far as the 5′-end of the mRNA molecule [ 22].
Use the SMART method to create actionable goals.
To probe the heterogeneous cellular composition of the P1 cell fraction, we randomly harvested single-cells from the P1 fraction and carried out reverse transcription using the Smart-seq2 method, followed by qPCR validation with several NSC/NPC markers, such as Prom1, Gfap, Dlx2, and Dcx.
cDNA was synthesized using the SMART PCR cDNA amplification method (Clontech) with a NotI oligo-dT primer (5' AACTGGAAGAATTCGCGGCCGCAGGAATTTTTTTTTTTTTTTTTT).
J. curcas root tissue samples treated at 150 mM, for 2 h time point were used in construction of cDNA libraries using the SMART cDNA synthesis Kit [ 18] (see Methods).
RNA was prepared using the method described previously [ 49] and reverse transcribed using the SMART PCR cDNA Synthesis Kit (Clontech, Mountain View, CA).
These sequences were then verified using the SMART tool (http://smart.embl-heidelberg.de/) [ 37].
Protein domain boundaries were identified using the SMART protein prediction database (http://smart.embl-heidelberg.de/).
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