Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Embryo
Cell type
Embryonic retina
NA
NA

Attributes by original data submitter

Sample

source_name
retina
strain
C57BL/6
developmental stage
embryonic day 17.5
tissue
retina

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
ATAC-seq library preparation was performed as described (Buenrostro et al., 2013) with minor modifications. Briefly, for each experiment, 2 × 105 - 5 × 105 dissociated retinal cells were washed twice with PBS (Lonza, 17-516F) containing Proteinase Inhibitor Cocktail (Sigma-Aldrich P8340), incubated with 50 μL of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.3% IGEPAL CA-630) on ice for 10 min and centrifuged at 500 g for 10 min at 4°C. After centrifugation, the pellet was immediately incubated with 50 μL of Tn5 transposition reaction mix (25 μL TD buffer, 2.5 μL TDE1 (Nextera DNA Library Prep Kit, Illumina, FC-121-1030) and 22.5 μL nuclease-free water) at 37°C for 30 min. After purification with QIAGEN MinElute PCR Purification Kit (QIAGEN, 28006), transposed DNA fragments were amplified with NEBNext High-Fidelity 2 × PCR Master Mix (New England Biolabs, M0541) for 5 cycles using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. 5 μL of each library was amplified in a 25 μL qPCR reaction with KAPA SYBRFAST qPCR Kit (Kapa Biosystems, KK4603) to estimate the optimum number of additional cycles to finish amplification of the remaining 45 μL library.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
162342790
Reads aligned (%)
74.1
Duplicates removed (%)
34.2
Number of peaks
43144 (qval < 1E-05)

mm9

Number of total reads
162342790
Reads aligned (%)
74.1
Duplicates removed (%)
34.2
Number of peaks
43086 (qval < 1E-05)

Base call quality data from DBCLS SRA