Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Embryo
Cell type
E8.5 posterior part
NA
NA

Attributes by original data submitter

Sample

source_name
E8.5 embryo_posterior part
strain background
Bl6
age
E8.5
genotype/variation
deltaC
tissue
posterior part

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Cells were isolated in PBS supplemented with 10% Fetal Calf Serum. ATAC experiments were performed according to Buenrostros et al., (2013) protocol and using a homemade transposome from Picelli et al., (2014). 7-8 embryos at 10-12s were dissected in cold PBS for each genotype and cells were mechanically dissociated. Cells were lysed before transposition using 1µL of transposome and purified using a Qiagen MinElute Kit with 10µL of Elution Buffer. Transposed DNA was amplified by PCR as previously described and quantified by qPCR using 5µL of PCR products. The number of additionnal cycles is determined by plotting linear Rn versus cycle and correspond to the one-third of the maximum fluorescence intensity. The remaining 45µL of PCR products are runned with the additional number of cycles. The final product is purified with Qiagen PCR Cleanup Kit and eluted in 20µL Elution Buffer. Sequencing was done on multiplexed samples using 42 bp Paired-end reads on the Illumina NextSeq system according to the manufacturer’s specifications at the genomics platform of IBENS.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
85454839
Reads aligned (%)
96.6
Duplicates removed (%)
11.8
Number of peaks
48844 (qval < 1E-05)

mm9

Number of total reads
85454839
Reads aligned (%)
96.5
Duplicates removed (%)
11.9
Number of peaks
48805 (qval < 1E-05)

Base call quality data from DBCLS SRA