Illumina ChIP-seq Library Preparation

Libraries were prepared using NEBNext Ultra II kits (NEB) following the manufacturer’s protocol. Following library preparation, ChIP samples were purified as described [30 (link)], while input samples were purified using a 2:1 ratio of AmpureXP (GE) beads to library. Following PCR amplification, all samples were purified using AMpure XP beads with 0.9:1 beads to PCR ratio. Samples were sequenced using the Illumina NextSeq 500 platform with paired ends. See S3 and S4 Tables for library statistics.

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Dukaj L, & Rhind N. (2021). The capacity of origins to load MCM establishes replication timing patterns. PLoS Genetics, 17(3), e1009467.

Publication 2021

NEBNext Ultra II kits AmpureXP NextSeq 500 platform

Chip Library

Corresponding Organization : University of Massachusetts Chan Medical School

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Variable analysis

independent variables

Library preparation using NEBNext Ultra II kits
Purification of ChIP samples as described [30]
Purification of input samples using a 2:1 ratio of AmpureXP beads to library
PCR amplification followed by purification using AMpure XP beads with 0.9:1 beads to PCR ratio
Sequencing using the Illumina NextSeq 500 platform with paired ends

dependent variables

Not explicitly mentioned

control variables

Not explicitly mentioned

positive controls

Not specified

negative controls

Not specified

Annotations

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