README: Antibody production relies on the tRNA inosine wobble modification to meet biased codon demand

tRNA sequencing of murine B cell lines

Description of the data and file structure

tRNA sequencing (2 independent sequencing runs)

Raw sequencing files from small RNA extracts processed using the AQRNAseq pipeline. RNA extracted from two PC-like murine cell lines (J558, MPC11) and two NBC-like murine cell lines (WEHI231, Bcl clone 5b1b)

Samples are numbered as follows:

Sequencing files are unpaired, the _1 or _2 following the file tag number represents the pairing info.

Code/Software

As described in the "Analysis of tRNA sequences by the AQRNA-seq pipeline" section of Methods and Materials:

Broadly, sequences underwent quality control, then were assembled using PEAR v0.9.6 and trimmed with fastxtoolkit.

Assembled sequences were aligned to a reference library composed of the GtRNAdb Mus musculus (GRCm38/mm10) high confidence tRNA gene set with Bowtie2. Parameters were as follows: bowtie2 -x db-tRNAgenome -k 100 --very-sensitive --ignore-quals --np 5 --reorder -p 20 -U seq.fa -f > seq_bt2.fa

For identification of wobble position mismatches, reads were aligned to the high confidence tRNA gene set using Python:
pairwise2.align.globalms(trna, read, 2, 1, -8, -0.5, penalize_end_gaps=False) using the Bio.pairwise2 module. The highest scoring alignment was chosen.

Differential expression was calculated using DESeq2.