Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Blood
Cell type
Loucy
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Lymphocytic

Attributes by original data submitter

Sample

source_name
LOUCY leukemia cell line
tissue
Leukemia cell line
cell line
LOUCY
chip antibody
H3K27ac (Diagenode, C15410196)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
5 million cells were used per sample. Cells were fixed with 1% formaldehyde for 10 min. Fixed chromatin was fragmented using an S220 Focused-ultrasonicator (Covaris) to an average size of 200-500 bp. Immunoprecipitation was then performed using a mixture of Protein A and Protein G Dynabeads (Life Technologies). Fragmented Drosophila melanogaster DNA was added at the immunoprecipitation step at a ratio of DNA from 1 Drosophila cell to 4 mouse/human cells, for the purpose of normalization (Orlando et al., Quantitative ChIP-Seq normalization reveals global modulation of the epigenome. Cell Rep 2014). However, reads mapping to the Drosophila melanogaster genome were not used for analysis. The NEBNext Ultra II DNA Library Prep Kit for Illumina, with NEBNext Multiplex Oligos for Illumina (New England BioLabs) was used to prepare DNA samples for sequencing as directed. Sequencing was performed using the Illumina NextSeq 500 platform.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
13780802
Reads aligned (%)
93.6
Duplicates removed (%)
1.8
Number of peaks
9303 (qval < 1E-05)

hg19

Number of total reads
13780802
Reads aligned (%)
93.0
Duplicates removed (%)
1.9
Number of peaks
9290 (qval < 1E-05)

Base call quality data from DBCLS SRA