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Refseq exons and micro RNA tracks were downloaded from the UCSC Genome Browser server and intersectBed from bedtools was applied to compare the reference data with the experimental data sets [ 48].
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Nelles, D.A. et al. Programmable RNA tracking in live cells with CRISPR/Cas9.
Endogenous RNA tracking reveals that RNA granules dock at sites of branch emergence and invade stabilized branches.
The y-axis of the RNA-Seq tracks represents raw read counts.
Error bars represent s.d., n = 2. d, RNA-seq tracks depicting the expression of the ΔNp63 isoform in the p63WT and p63KO day 7 cells.
The positions of the libra locus together with that of the adjacent annotated upstream and downstream loci are indicated, and the corresponding H3K4me3 ChIP-Seq, 3P-Seq and RNA-Seq tracks from wild type, libradel and librainv zebrafish are shown.
Pair-end RNA-seq tracks provided by California Institute of Technology (Caltech) were used for our analysis [ 42].
The RNA-seq tracks are displayed in the 'full view' (Expression panels, Fig. 1), whereas other tracks are displayed in the dense view.
Interestingly, the RNA-seq tracks show a lack of expression of the surrounding ZBED3- AS1 gene, implying that the SE is likely acting on a distant gene.
Units are in tags per million, with the exception of the RNA-seq tracks in Fig. 2c, d, Fig. 3c, and e, which are in units of tags per total mapped reads.
The respective Caltech GM12878 RNA-Seq track has been accessible through the UCSC genome browser [ 27, 28] since August 2012 and so far no unusual features of this dataset, including a possible progression towards a tumor line, have been reported.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com