Truseq nano dna 350 kit

Isolated gDNA from an ear sample of the transgenic piglet was sequenced on a HiSeqX Ten system (Illumina, San Diego, CA, USA). The sequencing library was constructed using the TruSeq Nano DNA (350) kit (Illumina, San Diego, CA, USA). Briefly, the gDNA sample was randomly fragmented and ligated with adapter, and then adapter-ligated fragments were amplified and gel purified. Paired-end sequencing was performed with 150bp read length, and raw data were processed using the Real Time Analysis 2 (RTA 2) software (Illumina, San Diego, CA, USA). The base calls (BCL) binary was converted into FASTQ using bcl2fastq v2. 15.0 (Illumina, San Diego, CA, USA). Clean reads (over 60× depth) were mapped to the current pig genome assembly (Sscrofa 10.2) and to the sequence of transgenic construct using the Hisat 2 software [30 (link)] with default options.

We collected 40 saliva samples from males in six European Roma populations (Lithuania, Spain, Macedonia Balkan, Ukraine Romungro, Hungary Romungro and Hungary Vlax). DNA was extracted using a standard phenol–chloroform procedure. Library preparation and sequencing were done in Macrogen Facility (Seoul, Korea), with TruSeq Nano DNA (350) kit and whole-genome shotgun paired-end sequencing (Illumina HiSeq X Ten) to a mean coverage of 29X (Supplementary Table S1). Roma individuals were selected for having all four grandparents belonging to the same geographical and sociocultural population. Additionally, 36 Roma males from Romania were included (Dobon B et al., in submission). As a reference panel, 28 European, 23 West Asian, 73 South Asian and 2 North African samples were used, only males were included in MSY analyses (Supplementary Table S2).

To build the genomic library, 1.0 µg g of DNA was used as input material for sample preparation. The DNA library was constructed using the Illumina TruSeq Nano DNA 350 Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations. The library was initially prepared via the random fragmentation of DNA samples to a size of 350 bp, followed by ligation to 5′ and 3′ adapters. The adapter-ligated fragments were then amplified via PCR and subjected to gel purification. To verify the size of the PCR-enriched fragments, the template size distribution was checked with an Agilent Technologies 2100 Bioanalyzer using a DNA 1000 chip (Agilent Technologies, Santa Clara, CA, USA). The prepared libraries were quantified using qPCR in accordance with the Illumina qPCR Quantification Protocol Guide (Illumina, San Diego, CA, USA).