Antigen

Antigen Class

RNA polymerase

Antigen

RNA polymerase II

Cell type

Cell type Class

Embryo

Cell type

Embryos

NA

NA

Sample

source_name

embryos

genotype

wt

embryos hand-sorted or not

sorted

chip antibody

8WG16 (Covance #MMS-126R)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Nuclei were collected from homogenized embryos and sonicated. Protein-DNA complexes, which are in the supernatant after sonication and centrifugation, were isolated with antibodies corresponding to each ChIP experiment. Libraries were prepared from ChIP and input DNA using the NEBNext® DNA Library Prep Master Mix Set for Illumina® kit (#E6040) either following the manufacturer’s instructions, or with a modified protocol using biotin-labeled dATP (Chen et al., 2013).

Sequencing Platform

instrument_model

Illumina HiSeq 2000

dm6

Number of total reads

11988884

Reads aligned (%)

99.5

Duplicates removed (%)

0.0

Number of peaks

3512 (qval < 1E-05)

dm3

Number of total reads

11988884

Reads aligned (%)

99.5

Duplicates removed (%)

0.0

Number of peaks

3487 (qval < 1E-05)