Why do I see  a poly(T) stretch at the 3' end of Read1 sequence?

A small proportion of the PCR products in the final library may have short inserts. In these cases, the sequencing from Read 1 will read through the T-tail added during library synthesis.ChIP-seq and small RNA-seq [...]

Do I need to trim DNA SMART ChIP reads prior to mapping?

You should trim three nucleotides from the 5' end of your reads (Read 1). Optionally, you may also trim Illumina adapter sequences and stretches of poly(T), particularly if you read more than 50 nucleotides, as sequences from short inserts will contain the T-tail that is added in the library construction process.ChIP-seq and small RNA-seq [...]

Can I perform paired-end sequencing of the DNA SMART ChIP library?

Single-end sequencing with Read 1 is generally sufficient for ChIP-seq. However, if paired-end sequencing is desired, we recommend using the DNA SMART Custom Read2 Seq Primer provided in the kit, that will allow sequencing to start right after the priming site of the DNA SMART Poly(dA) Primer, thus avoiding reading through the A/T tail created on the 3’ end of ssDNA molecules. Sequencing [...]

What is the advantage of the DNA SMART™ ChIP-Seq Kit?

Ligation-independent DNA library construction, compatible with 0.1–10ng double-stranded or single-stranded DNA (DNA recovered from ChIP assay may contain single-stranded DNA) employing a single post-PCR purification/ size selection generates higher DNA yield and higher library complexity than the competitive methods Please, see the Tech Note - Ligation-Free ChIP-Seq Library [...]

What is the advantage of a combined post-PCR purification/ size selection used in the DNA SMART™ ChIP-Seq Kit?

A simplified workflow of post-PCR size selection improved both library complexity (non-redundant rate) and yield – see Fig. 3 of the ABRF poster Template-switching technology for preparation of low-input ligation-free sequencing libraries (ABRF, March 2015)ChIP-seq and small RNA-seq [...]