Cell-free DNA was extracted from plasma using QIAamp Circulating Nucleic Acid kit (Qiagen). Sequencing libraries were prepared with the TruSeq ChIP preparation kit (Illumina, Foster City, CA) and sequenced using HiSeq 2500 instrument (Illumina) (Data Supplement ).
Truseq chip preparation kit
Manufactured by Illumina
The TruSeq ChIP preparation kit is a laboratory equipment designed to facilitate the chromatin immunoprecipitation (ChIP) process. It provides the necessary reagents and protocols to prepare DNA samples for sequencing analysis, allowing researchers to study protein-DNA interactions within a cell.
Automatically generated - may contain errors
Lab products found in correlation
Hiseq 2500 instrument, by Illumina (2 mentions)
Qiaamp circulating nucleic acid kit, by Qiagen (2 mentions)
Mouse anti h3k27me3 antibody, by Abcam (2 mentions)
Ipure beads v2, by Diagenode (2 mentions)
Ideal chip seq kit for transcription factors, by Diagenode (2 mentions)
Rabbit anti h3k4me1 antibody, by Ozyme (2 mentions)
Nextseq 500 platform, by Illumina (2 mentions)
Bioruptor pico sonicator, by Diagenode (2 mentions)
4 protocols using truseq chip preparation kit
1
Plasma cell-free DNA extraction and sequencing
2
ChIP-seq analysis of oligodendrocytes
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ChIP-seq assays were performed as described previously (Marie et al., 2018 (link)) using iDeal ChIP-seq kit for Transcription Factors (Diagenode, C01010055). Briefly, O4+ MACSorted cells were fixed in 1% formaldehyde (EMS, 15714) for 10 min at RT and the reaction was quenched with 125 mM glycine for 5 min at RT. Lysates were sonicated with a Bioruptor Pico sonicator (Diagenode, total time 8 min) and 4 μg of antibodies were added to sheared chromatin (from 4 million cells for Olig2 and from 1 million cells for histone marks) and incubated at 4°C overnight on 10 rpm rotation. Antibodies used were mouse anti-Olig2 antibody (Millipore, MABN50), rabbit anti-H3K4me3 antibody (Active Motif, 39060), rabbit anti-H3K27Ac antibody (Active Motif, 39034), rabbit anti-H3K4me1 antibody (Ozyme, 5326T), and mouse anti-H3K27me3 antibody (Abcam, ab6002). Mock (rabbit IgG) was used as negative control. Chromatin-protein complexes were immunoprecipitated with protein A/G magnetic beads and washed sequentially according to the manufacturer (Diagenode, C01010055). DNA fragments were then purified using IPure beads v2 (Diagenode, C01010055). Input (non-immunoprecipitated chromatin) was used as control in each individual experiment. The ChIP-seq libraries were prepared using Illumina TruSeq ChIP preparation kit and sequenced with Illumina NextSeq 500 platform.
3
Cell-free DNA Extraction and Sequencing
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Cell-free DNA was extracted from plasma using QIAamp Circulating Nucleic Acid kit (Qiagen). Sequencing libraries were prepared with the TruSeq ChIP preparation kit (Illumina, Foster City, CA) and sequenced using HiSeq 2500 instrument (Illumina) (Data Supplement).
4
Chromatin Immunoprecipitation Sequencing
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ChIP-seq assays were performed as described previously (Marie et al; 2018) , using iDeal ChIPseq kit for Transcription Factors (Diagenode, C01010055). Briefly, O4 + MACSorted cells were fixed in 1% formaldehyde (EMS, 15714) for 10 min at room temperature and the reaction was quenched with 125 mM glycine for 5 min at room temperature. Lysates were sonicated with a Bioruptor Pico sonicator (Diagenode, total time 8 min) and 4μg of antibodies were added to sheared chromatin (from 4 million cells for Olig2 and from 1 million cells for histone marks) and incubated at 4°C overnight on 10 rpm rotation. Antibodies used were: mouse anti-Olig2 antibody (Millipore, MABN50), rabbit anti-H3K4me3 antibody (Active motif, 39060), rabbit anti-H3K27Ac antibody (Active motif, 39034), rabbit anti-H3K4me1 antibody (Ozyme, 5326T), mouse anti-H3K27me3 antibody (Abcam, ab6002). Mock (Rabbit IgG) was used as negative control. Chromatin-protein complexes were immunoprecipitated with protein A/G magnetic beads and washed sequentially according to the manufacturer (Diagenode, C01010055). DNA fragments were then purified using IPure beads v2 (Diagenode, C01010055). Input (nonimmunoprecipitated chromatin) was used as control in each individual experiment.
The ChIP-seq libraries were prepared using ILLUMINA Truseq ChIP preparation kit and sequenced with ILLUMINA Nextseq 500 platform.
The ChIP-seq libraries were prepared using ILLUMINA Truseq ChIP preparation kit and sequenced with ILLUMINA Nextseq 500 platform.
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