Antigen

Antigen Class

Input control

Antigen

Input control

Cell type

Cell type Class

Embryo

Cell type

Neural tube

NA

NA

Sample

source_name

Neural tube

developmental stage

E11.5

strain

Prdm13fusionGFP

antibody

none (input)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

For full ChIP protocol see Meredith 2013 MCB 33:3166-3179. For extraction, nuclei were liberated from neural tube tissue by dounce homogenization in PBS and then fixed in 1% formaldehyde for 10 minutes at room temperature. Fixation was terminated by adding glycine to a final concentration of 0.125M. Chromatin was sheared using a Diagenode Bioruptor for 30 minutes on high power with 30s:30s on:off cycles. 100 μg chromatin was immunoprecipitated with 5 μg rabbit anti-PRDM13 antibody (Johnson Lab generated, PA6659, rabbit anti-mouse PRDM13) followed by anti-mouse Dyna beads (Invitrogen). Libraries were made according to Illumina's ChIP-seq DNA sample prep protocol

Sequencing Platform

instrument_model

Illumina HiSeq 2500

mm10

Number of total reads

27097906

Reads aligned (%)

78.4

Duplicates removed (%)

11.5

Number of peaks

510 (qval < 1E-05)

mm9

Number of total reads

27097906

Reads aligned (%)

78.2

Duplicates removed (%)

11.5

Number of peaks

547 (qval < 1E-05)