Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
G1E-ER4+E2
Tissue
Blood
Lineage
cellLine
Description
Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

Attributes by original data submitter

Sample

source_name
724_Async_input
cell line
G1E ER4
treatment
estradiol 13h
transgene
stably expressing YFP-MD
nocodazole
asynchronous
antibody
input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
All samples, including input, were processed for library construction for Illumina sequencing using Illumina’s TruSeq ChIP Sample Preparation Kit (Illumina cat# IP-202- 1012). In brief, DNA fragments were repaired to generate blunt ends, purified using Agencourt AMPure XP Beads (Beckman Coulter cat# A63881), and a single “A” nucleotide was added to each end. Double-stranded Illumina adaptors were ligated to the fragments. Ligation products were purified using Agencourt AMPure XP Beads, and subject to size selection using SPRIselect Beads (Beckman Coulter cat# B23318)in which both a left side size selection was performed at 0.9x volume, and a right side size selection was performed at 0.6x volume according to manufacturer’s specifications. Library fragments were then amplified for 16 cycles of PCR and products were purified using Agencourt AMPure XP Beads. Constructed libraries were run on the Agilent Bioananlyzer 2100 (Agilent Technologies) using either the DNA 7500 kit (cat# 5067-1504) or the High Sensitivity DNA kit (cat# 5067-4626) as appropriate to determine the average size and confirm the absence of unligated adaptors. The mean library size is approximately 330 bp. The ChIP-seq libraries were quantitated by qPCR using the Kapa SYBR FAST Universal kit (Kapa Biosystems) according to the Illumina’s Sequencing Library qPCR Quantification Guide. Libraries were multiplexed and sequenced on the Illumina HiSeq 2000 using Illumina’s kits and reagents as appropriate. We sequenced 3 biological replicates for the 0min, 60min, 90min, 180min, and 360min time points; two biological replicates for 240min time point; and one replicate for 40min time point.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
55619481
Reads aligned (%)
97.3
Duplicates removed (%)
15.2
Number of peaks
485 (qval < 1E-05)

mm9

Number of total reads
55619481
Reads aligned (%)
97.0
Duplicates removed (%)
15.2
Number of peaks
572 (qval < 1E-05)

Base call quality data from DBCLS SRA