ChIP-seq was conducted similarly to ChIP, except that chromatin was isolated from a 600 mL early log culture of BY4741 cells (either NHS or 5 min heat-shocked) and sonicated for 60 cycles. A 10% fraction of the total chromatin was immunoprecipitated using the anti-Hsf1 antibody. The Hsf1-ChIP libraries were generated using 5 ng of the purified ChIP DNA (ChIP-seq Sample Prep Kit, New England Biolabs). Libraries were sequenced using an Illumina MiSeq genome sequencer. To generate normalized UCSC tracks, we combined the replicate aligned BAM files and called peaks with MACS2 using the -B option. Since these were paired-end libraries (-BAMPE), the fragment size was measured directly from the data and MACS2 reported the pileup aligned reads using the insert size from the paired-end BAM file. As a default, the bedGraphs were not normalized by read depth but each bedGraph coordinate intensity was multiplied by a normalization factor (10 million divided by total fragments in the library).
Chip seq sample prep kit
Manufactured by New England Biolabs
The ChIP-seq Sample Prep Kit is a tool used to prepare DNA samples for chromatin immunoprecipitation sequencing (ChIP-seq) analysis. The kit provides the necessary reagents and protocols to perform the initial steps of the ChIP-seq workflow, including chromatin shearing, immunoprecipitation, and DNA purification.
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Lab products found in correlation
2 protocols using chip seq sample prep kit
1
Hsf1 ChIP-seq in Yeast Heat Shock
2
Hsf1 ChIP-seq in Yeast Heat Shock
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ChIP-seq was conducted similarly to ChIP, except that chromatin was isolated from a 600 mL early log culture of BY4741 cells (either NHS or 5 min heat-shocked) and sonicated for 60 cycles. A 10% fraction of the total chromatin was immunoprecipitated using the anti-Hsf1 antibody. The Hsf1-ChIP libraries were generated using 5 ng of the purified ChIP DNA (ChIP-seq Sample Prep Kit, New England Biolabs). Libraries were sequenced using an Illumina MiSeq genome sequencer. To generate normalized UCSC tracks, we combined the replicate aligned BAM files and called peaks with MACS2 using the -B option. Since these were paired-end libraries (-BAMPE), the fragment size was measured directly from the data and MACS2 reported the pileup aligned reads using the insert size from the paired-end BAM file. As a default, the bedGraphs were not normalized by read depth but each bedGraph coordinate intensity was multiplied by a normalization factor (10 million divided by total fragments in the library).
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