ChIP-Seq libraries were prepared from a total of 10 ng DNA using TruSeq Nano DNA Sample Prep Kit (Illumina, USA) according to the manufacturer’s instructions. The completed libraries were quantified by 2100 Bioanalyzer (Agilent, Waldbronn, Germany). The libraries were then sequenced by running 2 × 150 cycles on the Illumina HiSeq 4000 following the HiSeq 3000/4000 SBS Kit protocol (Illumina). After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software V1.8. Sequence quality was examined using the FastQC software. After passing Solexa CHASTITY quality filter, the clean reads were aligned to Rat genome (UCSC RN5) using BOWTIE software V2.1.0.21 (link) The MACS V1.4.2 program22 (link) was then used for peak calling of the ChIP enrichment regions relative to control data set that was generated from input samples. The peaks in samples were annotated by the nearest gene using the newest UCSC RefSeq database.
Hiseq 3000 4000 sbs kit protocol
Manufactured by Illumina
The HiSeq 3000/4000 SBS Kit protocol is a laboratory equipment product designed for use with Illumina's HiSeq 3000 and HiSeq 4000 sequencing systems. The protocol provides the necessary reagents and instructions for performing sequencing-by-synthesis (SBS) reactions, which is the core function of the product.
Automatically generated - may contain errors
2 protocols using hiseq 3000 4000 sbs kit protocol
1
ChIP-Seq Library Preparation and Analysis
2
ChIP-seq for Genome-wide Profiling
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ChIP-seq libraries were prepared from a total of 10 ng DNA using TruSeq Nano DNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions. The completed libraries were quantified by 2100 Bioanalyzer (Agilent, Waldbronn, Germany). The libraries were then sequenced by running 2 × 150 cycles on the Illumina HiSeq 4000 following the HiSeq 3000/4000 SBS Kit protocol (Illumina). After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using the Off-Line Basecaller software V1.8. Sequence quality was examined using the FastQC software. After passing Solexa CHASTITY quality filter, the clean reads were aligned to Rat genome (UCSC RN5) using the BOWTIE software V2.1.0 [25 (link)]. The MACS V1.4.2 program [26 (link)] was then used for peak calling of the ChIP enrichment regions relative to control data set that was generated from input samples. The peaks in samples were annotated by the nearest gene using the newest UCSC RefSeq database.
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