Antigen

Antigen Class

Input control

Antigen

Input control

Cell type

Cell type Class

Epidermis

Cell type

Carcinoma, Basal Cell

MeSH Description

A malignant skin neoplasm that seldom metastasizes but has potentialities for local invasion and destruction. Clinically it is divided into types: nodular, cicatricial, morphaic, and erythematoid (pagetoid). They develop on hair-bearing skin, most commonly on sun-exposed areas. Approximately 85% are found on the head and neck area and the remaining 15% on the trunk and limbs. (From DeVita Jr et al., Cancer: Principles & Practice of Oncology, 3d ed, p1471)

Sample

source_name

BCC

cell type

BCC from tail epidermis

tumor stage

9 weeks post tamoxifen

genotype

R26-SmoM2/+ K14CreER

chip antibody

none

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Chromatin was fragmaneted with sonicaiton and precleared prior to overnight incubation with specific antibodies Library was prepared using NEBNext® Ultra DNA Library Prep Kit and NEBNext® Multiplex Oligos for Illumina (NEB) according to the manufacturer's recommendations DNA extraction and chromatin immunoprecipitation were performed as previously described in Galli et al., 2012 doi 10.1016/j.molcel.2015.09.001 Libraries for ChIP-sequencing were generated by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) and barcoding added using NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (NEB) according to the manufacturer's recommendation.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

24414237

Reads aligned (%)

83.3

Duplicates removed (%)

45.3

Number of peaks

11418 (qval < 1E-05)

mm9

Number of total reads

24414237

Reads aligned (%)

82.7

Duplicates removed (%)

45.2

Number of peaks

11345 (qval < 1E-05)