Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Kidney
Cell type
mpkCCD
NA
NA

Attributes by original data submitter

Sample

source_name
mpkCCD cells
cell type
cultured mouse collecting duct cells (mpkCCD)
passages
6 to 10
strain
transformed mouse renal principal cells
chip antibody
anti-IGG antibody (Catalog #:2729)
treatment
dDAVP (0.1 nM)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The mpkCCD cells cross-linking (formaldehyde 1.11%), nuclei were isolated and then sheared into approximately 300-bp fragments (Covaris S2 SonoLAB). Samples underwent chromatin immunoprecipitation (SimpleChIP protocol (#9003, Cell Signaling Technology) using the anti-Polr2a antibody (Catalog #: MMS-126R, Covance). After the ChIP step, crosslinking was reversed and samples were processed for library construction. The libraries were made using an Ovation Ultralow Library System (NuGen). cDNAs ranging from 200 to 400 bp were selected on 2% agarose gel and sequenced on a HiSeq2000 platform (Illumina) to generate 50-bp FASTQ sequences. The raw FASTQ sequences were mapped to the mouse Reference Genome (mm10) using the Burrows-Wheeler Aligner (BWA).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
25627898
Reads aligned (%)
95.9
Duplicates removed (%)
15.5
Number of peaks
177 (qval < 1E-05)

mm9

Number of total reads
25627898
Reads aligned (%)
95.6
Duplicates removed (%)
15.5
Number of peaks
397 (qval < 1E-05)

Base call quality data from DBCLS SRA