Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Zmynd8

Cell type

Cell type Class
Blood
Cell type
CH12
Tissue
Blood
Lineage
cellLine
Description
B-cell lymphoma (GM12878 analog)

Attributes by original data submitter

Sample

source_name
CH12 cells
cell type
CH12 cells
genotype
WT
antibody
ZMYND8 (HPA020949, Sigma-Aldrich)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-Seq for ZMYND8 and RNA Pol II were performed as it follows. Splenocytes (72 h post-activation) or CH12 cells (48 h post-activation) were fixed with 1% (16% Formaldehyde Methanol-free, Thermo Scientific) at 37°C for 10 min followed by addition of 1/20 volume of 2.5 M glycine (dissolved in PBS pH 7.4) and swirling. Fixed cells were washed with cold PBS,centrifuged and aliquoted. 20 million cells were resuspended in 100 ul of 1% SDS of RIPA buffer supplemented with Complete EDTA free proteinase inhibitor (Roche) and sonication was performed with a Covaris S220 Focused Ultrasonicator at peak value 105, duty factor 5, cycle/burst 200 for 10 minutes. After sonication, samples were adjusted to 0.1% SDS final concentration by diluting with non-SDS containing RIPA buffer. Chromatin fragments were then pre-cleaned by incubation with Dynabeads Protein A (Invitrogen) with rotation at 4°C for 1 h, and immunoprecipitated with antibody-bound Dynabeads. 10 ug antibodies specific for ZMYND8 (Sigma-Aldrich) or RNA Pol II polymerase (4H8, Abcam) were used for each sample. DNA libraries were prepared by using Illumina compatible adaptors (Bio Scientific) and sequenced on an Illumina NextSeq 500 Sequencer.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
97210520
Reads aligned (%)
20.7
Duplicates removed (%)
7.1
Number of peaks
2097 (qval < 1E-05)

mm9

Number of total reads
97210520
Reads aligned (%)
20.7
Duplicates removed (%)
7.2
Number of peaks
2063 (qval < 1E-05)

Base call quality data from DBCLS SRA