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Comparison of barcode read counts revealed no significant difference between the two experimental procedures (see Supplementary Table S1).
The barcode read counts of DNA spike-ins were increased in a dose-dependent manner, indicating that our method works quantitatively (Fig. 1C).
"No merchant I have tried has been able to scan my phone to get the barcode," read the first review on Amazon's page for the app (which you can still see by way of a Google cache).
We obtained at least one barcode read for 2563 deletion mutants and could determine reliable CLS data for 1199 of these mutants (Table S3).
Sequencing on the HiSeq2500 platform (Illumina) involved 101 cycles for read1, 7 cycles for the barcode read, and 101 cycles for read2.
Here we report a set of 384 barcodes with an edit distance of 5 between any two members, allowing single base error correction, three base error detection and requiring at least 4 sequencing errors in the barcode read before being mistaken for an alternative barcode.
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The multimer reagent pool was used as the baseline to determine the number of DNA barcode reads within a non-processed MHC multimer reagent library.
To determine the read count value for each sgRNA, the trimmed barcode reads were next mapped to custom sgRNA reference library using Bowtie2 (version 2.1.0) with option -L 22 -N 0 -k 1.
Fastq files were generated by "debarcoding" genomic reads using the associated barcode reads; reads for which barcodes yielded no exact match to an expected barcode, or contained one or more low-quality base calls, were discarded.
Here we used only the perfect matching barcode reads to sort the sequencing reads to according to their sample identity, leaving a subset of reads un-assigned (data not shown).
Reassuringly, barcode reads for deletion mutants in genes reported to be necessary for entry into or maintenance of quiescence (Sajiki et al. 2009) were either absent or present at very low numbers (<10) throughout the time course (Table S2).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com