Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SETD1A

Cell type

Cell type Class
Blood
Cell type
Erythroid Cells
MeSH Description
The series of cells in the red blood cell lineage at various stages of differentiation.

Attributes by original data submitter

Sample

source_name
R3/R4 Erythroid cells
cell type
R3/R4 Erythroid cells
chip antibody
SET1
antibody info
Bethyl Laboratory Cat#: A300-289A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP libraries were prepared using the KAPA Library Preparation Kit (KAPA Biosystems) per the manufacturer's protocol. Briefly, ChIP DNA was end repaired, followed by addition of an adenine base at the 3' and NEXTflex ChIP-Seq Barcodes (BiooScientific) adaptor ligation. The modified DNA was then size selected on a 2% agarose and purified by using a gel extraction kit (Qiagen). One microliter of size-selected adaptor ligated DNA was initially analyzed by SYBR Green Q-PCR to determine the number of cycles required to reach 50% of complete amplification. Adaptor ligated DNA was PCR amplified with one initial heating step of 98°C for 45 second, followed by the pre-determined number of cycles with a melting temperature of 98°C for 15 s, an annealing temperature of 65°C for 30 s, and a product extension at 72°C for 30 s. At the end of the amplification, a final extension at 72°C for 1 min was performed. Amplified ChIP DNA was subjected to deep sequencing using standard Yale Center for Genome analysis protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
33752255
Reads aligned (%)
86.6
Duplicates removed (%)
9.1
Number of peaks
6957 (qval < 1E-05)

hg38

Number of total reads
33752255
Reads aligned (%)
87.5
Duplicates removed (%)
8.6
Number of peaks
6988 (qval < 1E-05)

Base call quality data from DBCLS SRA