Table 1 Low-input library preparation methods tested in this study
From: A comparative study of ChIP-seq sequencing library preparation methods
Technique | Reference/Commercial supplier | Salient details | Reported DNA input range | Sequencing platform compatibility |
|---|---|---|---|---|
Accel-NGS® 2S (Accel-2S) | Swift Biosciences, Inc. | 5-step process of DNA repair, adapter ligation and PCR amplification. 5 purification steps. | 0.01 – 1000 ng | Illumina |
Modified Illumina method (Bowman) | Kingston Lab [36] | 4 step procedure of end-repair, A-tailing, adapter ligation and PCR. 4 purification steps. | 0.1 – 1000 ng | Illumina |
HTML-PCR (HTML) | Camilli lab [37] | 4-step procedure of end-repair, poly-C-tailing, poly-G-adapter oligo ligation and PCR. 4 purification steps. | 0.01 – 100 ng | Illumina |
SeqPlex™ | Sigma Aldrich, Inc. | 3-stage process of semi-random primed pre-amplification, PCR amplification, and primer removal. 2 purification steps. | 0.1 – 1 ng | Agnostic (subsequent library prep required) |
DNA SMART™ ChIP-Seq Kit (SMART) | Takara Bio USA, Inc. | 5-step procedure of denaturation, dephosphorylation, T-tailing, DNA replication and template switching by reverse transcriptase and PCR. Compatible also with ssDNA. 1 purification step. | 0.1 – 10 ng | Illumina |
TELP | Xu lab [38] | 5-step procedure of end-repair, poly-C-tailing, biotinylated primer extension, exonuclease digestion & streptavidin purification, adapter ligation and PCR. Compatible also with ssDNA. 3 purification steps. | 0.025–25 ng | Illumina |
ThruPLEX® | Rubicon Genomics | 3 stage process of end repair, stem-loop adapter ligation and PCR amplification. 1 purification step. | 0.05–50 ng | Illumina |