Hiseq x pe cluster kit v2

A total amount of 0.5 μg DNA per sample was used for the DNA library preparations. Sequencing library was generated using Truseq Nano DNA HT Sample Prep Kit (Illumina USA) following manufacturer’s recommendations and index codes were added to each sample. Briefly, genomic DNA sample was fragmented by sonication to a size of 350 bp. Then DNA fragments were end-polished, A-tailed, and ligated with the full-length adapter for Illumina sequencing, followed by further PCR amplification. After PCR products were purified (AMPure XP system), libraries were analyzed for size distribution by Agilent 2100 Bioanalyzer and quantified by real-time PCR (3 nM).
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using HiSeq X PE Cluster Kit V2.5 (Illumina) according to the manufacturer’s instructions. After cluster generation, the DNA libraries were sequenced on Illumina HiSeq platform and 150 bp paired-end reads were generated.

A total amount of 3 µg RNA of C42B or C42B KDM6B KD cell line was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNex^® UltraTMRNA Library Prep Kit for Illumina^® (NEB, USA), following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample. Clustering of the indexed samples was performed on a cBot Cluster Generation System using a HiSeq X PE Cluster Kit V2.5 (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. We then selected Hisat2 as the mapping tool for which Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. Differential expression analysis between C42B and C42B KDM6B KD (three biological replicates per condition) was performed using the DESeq2 R package (1.16.1). Genes with an adjusted P-value < 0.05 found by DESeq2 were assigned as differentially expressed. RNA-sequencing data were deposited into CNGB Sequence Archive (https://db.cngb.org/cnsa/) of CNGBdb with accession number CNP0001447.

A total of 0.5 μg of DNA per sample was used as input material for the DNA library preparations. Genomic libraries were prepared using the Illumina Truseq Nano DNA HT Sample Prep Kit following the manufacturer’s instructions. Libraries were analyzed for size distribution by Agilent 2100 Bioanalyzer. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using Hiseq X PE Cluster Kit V2.5 (Illumina, San Diego, CA, United States) according to the manufacturer’s instructions. Then, the DNA libraries were sequenced on the Illumina Hiseq platform and 150 bp paired-end reads were generated.

A total amount of 0.5 μg DNA per sample was used as input material for the DNA library preparations. Genomic libraries were prepared using the Illumina Truseq Nano DNA HT Sample Prep Kit following the manufacturer’s instructions. Libraries were analyzed for size distribution by Agilent 2100 Bioanalyzer. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using Hiseq X PE Cluster Kit V2.5 (Illumina, San Diego, CA, United States) according to the manufacturer’s instructions. Then, the DNA libraries were sequenced on Illumina Hiseq platform and 150 bp paired-end reads were generated.