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Sequence analysis was performed using the SOLiD System Small RNA Analysis Tool Life Technologiess) and MiRanalyzer [8].
To search for evidence of additional microRNAs in H1 human embryonic stem cell cultures (hESC), we prepared RNA samples for deep sequencing using the SOLiD system for massively-parallel sequencing by ligation [33], [34].
The whole transcriptome RNA libraries were constructed, following by deep sequencing using the SOLiD System (Applied Biosystems).
Additionally, using the SOLiD system and the SOLiD RNA Barcoding Kit (v4 chemistry), 1/4 run, in which all RNA samples were independently represented using barcodes, was performed.
Sequencing was performed using the SOLiD system producing a total of 108499924 filter passing reads (average reads per sample = 1937499 ± 788474 standard deviation).
Genomic DNA from a Black Angus bull and a Holstein bull were sequenced using the SOLiD system and a combination of fragment and mate pair libraries (Table 1).
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Because small RNAs derived from zma- MIR169e/h had not been previously reported (miRBase database: release 19, August 2012), we used the SOLiD system to sequence small RNAs from endosperm tissue derived from B73 and Mo17 cultivars and their reciprocal crosses; however, we could not detect small RNA reads derived from them, at least in endosperm tissue.
Libraries were prepared following the SOLiD™ System 2.0 User Guide and SOLiD™ 2 System Template Bead Preparation guide and sequenced using the SOLiD V2 system (Applied Biosystems).
Then, we resequenced the enriched products using the SOLiD 3.0 system platform (Life Technologies, Foster City, CA, USA).
ChIP-seq DNA fragment libraries were sequenced using the SOLiD 5500 system to produce 75-bpreads.
RNA-seq experiments were conducted using the SOLiD 5500×l system with the standard protocol.
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