Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
YBX1

Cell type

Cell type Class
Blood
Cell type
HEL
Primary Tissue
Blood
Tissue Diagnosis
Erythroleukemia

Attributes by original data submitter

Sample

source_name
HEL cultured cell line
cell line
HEL
chip target
YBX1
antibody
anti-YBX1 (Abcam, EP2708Y, #ab76149)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The cells were collected and washed twice in ice-cold PBS followed by crosslinking in 1% formaldehide (methanol free) for 5 minutes. Excess of formaldehyde was quenched by addition of Tris pH 8.0 to 100nM final and Glycine 125 mM final. Chromatin was cheared using Covaris E220 for 20 min with power 140; duty 5; bursts 200/sec. We then used 5ul aliquote of sherared chromatin to decrosslink in order to test completeness of shearing. Chromatin was considered passed QC if fragments 100-600bp were >90%. For immunoprecipitation we used aproximately chromatin from 1-10x10^6 cells, 5-10ug of specific antibody and 10-20ul of Protein-A/G magnetic beads (Dynal). In 16 hours the immune complexes were wased in Mixed Micelle Buffer, buffer 500, LiCl/detergent solution and TE buffers. DNA was eluted from the beads using 100mM NaHCO3 100mM NaCl 1% SDS and purified using AmpureXP beads. 1-10 ng of ChIP'ed DNA was used for Illumina compatible library generation using ThruPlex DNA-seq kit with 10 to 14 cycles of amplification with single end barcodes

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
20635665
Reads aligned (%)
101.2
Duplicates removed (%)
47.4
Number of peaks
6813 (qval < 1E-05)

hg38

Number of total reads
20635665
Reads aligned (%)
103.3
Duplicates removed (%)
46.8
Number of peaks
6491 (qval < 1E-05)

Base call quality data from DBCLS SRA