Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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.

Attributes by original data submitter

Sample

source_name
Patski cells
cell line
Patski cells
cell type
Fibroblasts derived from hybrid embryonic kidney
strain/background
BL6/spretus
genotype/variation
Del-hinge
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed using fixed chromatin from cell lines. DNA from ChIP pull-down chromatin fractions were de-crosslinked and purified using QIAquick PCR purification kit. Sequencing libraries were prepared from each CTCF ChIP sample from Patski cells using the Illumina seq sample prep kit. Size selection of the library was done by gel excision and purification of DNA in the 300-600bp range. Control sequencing library was prepared from genomic DNA.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
165137101
Reads aligned (%)
84.5
Duplicates removed (%)
40.3
Number of peaks
167307 (qval < 1E-05)

mm9

Number of total reads
165137101
Reads aligned (%)
84.2
Duplicates removed (%)
40.9
Number of peaks
167514 (qval < 1E-05)

Base call quality data from DBCLS SRA