Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryo
Cell type
Neural Crest
MeSH Description
Neuroectodermal cells of the neural crest. They differentiate into various cell types during EMBRYOGENESIS including craniofacial MESENCHYME; ENDOCRINE CELLS; MELANOCYTES and PERIPHERAL NERVOUS SYSTEM.

Attributes by original data submitter

Sample

source_name
Cranial Neural Crest
Stage
Embryonic day E12.5
tissue
Wnt1-Cre, Rosa-Tomato flow sorted cranial neural crest
genotype
Utx fl/fl, Wnt1-Cre: fko
Sex
female
antibody
Input, none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RNA isolation, cranial neural crest were sorted into Trizol LS and processed accordingly. For ChIP, sorted cranial neural crest were pelleted in PBS, frozen cell pellets were thawed, digested with Micrococcal Nuclease, and antibody ChIP isolated histone-DNA complexes. For O9-1 ChIP, cells were fixed with 0.3% Formaldehyde for 30 minutes at 4 degrees, nuclei were isolated by Dounce homogenization, digested with Micrococcal Nuclease, and antibody ChIP isolated histone-DNA complexes. RNA-seq: KAPA KK8420 Stranded mRNA-seq Kit for mRNA isolation, cDNA production, Illumina TruSeq adapter ligation, and library amplification. For ChIP-seq: KAPA KK8502 Hyper Prep Kit for Illumina TruSeq adapter ligation and library amplification.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
48596860
Reads aligned (%)
100.0
Duplicates removed (%)
3.9
Number of peaks
64 (qval < 1E-05)

mm9

Number of total reads
48596860
Reads aligned (%)
100.0
Duplicates removed (%)
4.0
Number of peaks
57 (qval < 1E-05)

Base call quality data from DBCLS SRA