Antigen

Antigen Class

Histone

Antigen

H3K27me3

Cell type

Cell type Class

Kidney

Cell type

Patski

Tissue

Kidney

Lineage

cellLine

Description

Mouse Embryonic Kidney Fibroblast. As described in Lingenfelter et al., 1998 (Nat Genet. 1998 18:212-3) and Yang et al., 2010 (Genome Res. 2010 20:614-22), PATSKI is a female interspecific mouse fibroblast that was derived from the embryonic kidney of an M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X. This is an adherent cell line.

Sample

source_name

H3K27me3 ChIP-seq experiment in CRISPR/cas9-modified Patski cells

strain

BL6/spretus

cell type

Fibroblasts derived from hybrid embryonic kidney

cell type

Patski cells

chip antibody

Anti-H3K27me3 Antibody (Rabbit Polyclonal Antibody; Upstate/Millipore, #07-449)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

ChIP was performed using fixed chromatin from Patski cells. DNA from ChIP pull-down chromatin fractions were de-crosslinked and purified using QIAquick PCR purification kit. Sequencing libraries were prepared each from three or four pooled independent ChIP samples from Patski cells using the Illumina seq sample prep kit. Size selection of the library was done by gel excision or two-step Ampure bead purification and purification of DNA in the 300-600bp range.

Sequencing Platform

instrument_model

NextSeq 500

mm10

Number of total reads

349845298

Reads aligned (%)

89.6

Duplicates removed (%)

24.7

Number of peaks

21600 (qval < 1E-05)

mm9

Number of total reads

349845298

Reads aligned (%)

89.5

Duplicates removed (%)

24.8

Number of peaks

21753 (qval < 1E-05)