Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC H9
NA
NA

Attributes by original data submitter

Sample

source_name
H9
cell type
human embryonic stem cells
cell line
H9
condition
CCDC144NL-AS1 KD
passages
35
chip antibody
H3K4me3 (Abcam, ab8580)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RNA-seq, total RNA of cells was extracted by RNAiso Plus (Takara), according to the manufactures' instructions. For ChIP-seq, lysates were clarified from sonicated nuclei and histone-DNA complexes isolated with antibody RNA libraries were prepared for sequencing using standard Illumina protocols. ChIP-seq libraries were prepared for sequencing using TruSeq Nano DNA Sample Prep Kit (Illumina), according to the manufacter's instructions.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
22051401
Reads aligned (%)
94.6
Duplicates removed (%)
16.9
Number of peaks
20611 (qval < 1E-05)

hg19

Number of total reads
22051401
Reads aligned (%)
94.2
Duplicates removed (%)
17.1
Number of peaks
20405 (qval < 1E-05)

Base call quality data from DBCLS SRA