Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
B cells
NA
NA

Attributes by original data submitter

Sample

source_name
mouse GC B cells
cell type
GC B splenocytes (GL7+Fas+B220+)
genotype/variation
LSD1 KO (C<gamma>1-Cre;Lsd1fl/fl)

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Fifty thousand purified GC B cells were resuspended in 1ml of ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water) and centrifuged at 500 r.c.f. and 4°C for 5 min. Supernatant was aspirated by pipetting and cells were resuspended in 50ul of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin and incubated on ice for 3 min. Following lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 was added, and nuclei were centrifuged at 500 r.c.f. and 4°C for 10 minutes. Supernatant was then aspirated by pipetting and nuclei were resuspended in 50 μl of transposition mix (25 μl 2× TD buffer, 2.5 μl tagment DNA enzyme, 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) and incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Zymo DNA Clean and Concentrator columns. DNA libraries were prepared as described (Corces et al. Nat. Methods, 2017) and sequenced on a Hi-Seq 2000 (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
29988795
Reads aligned (%)
94.1
Duplicates removed (%)
23.6
Number of peaks
32315 (qval < 1E-05)

mm9

Number of total reads
29988795
Reads aligned (%)
93.9
Duplicates removed (%)
23.7
Number of peaks
32269 (qval < 1E-05)

Base call quality data from DBCLS SRA