Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ascl2

Cell type

Cell type Class
Digestive tract
Cell type
Colonic epithelial stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
WT mCh+ Colon Stem Cell FLAG-Ascl2 ChIP-seq
strain background
C57BL/6 129/Sv mixed
genotype/variation
wild type
tissue
mouse colon epithelium
cell type
Mouse colon stem cells
cell population
Ascl2(mCh); Lgr5Dtr-Egfp
chip antibody
FLAG (Sigma-Aldrich, F1804, lot SLBN5629V)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Colonic epithelial cells were isolated in 10mM EDTA in DMEM, digested in a mixture of Accumax, Dispase, TrypLE , and sorted based on mCherry or GFP. RNA was extracted with Trizol reagent (ThermoFisher) for RNA-seq. Whole nuclei were used for chromatin transposition with Nextera Tn5 Transposase (Illumina) for ATAC-seq and ChiP-seq. SMARTer® Universal Low Input RNA Kit (TAKARA Bio) for RNA library and high-fidelity 2X PCR Master Mix (NEB) for ChIP and ATAC library were used.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
29872452
Reads aligned (%)
94.0
Duplicates removed (%)
41.4
Number of peaks
13005 (qval < 1E-05)

mm9

Number of total reads
29872452
Reads aligned (%)
93.8
Duplicates removed (%)
41.4
Number of peaks
12981 (qval < 1E-05)

Base call quality data from DBCLS SRA