Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pluripotent stem cell
Cell type
Embryoid Bodies
MeSH Description
Spontaneous aggregations of human embryonic stem cells that occur in vitro after culturing in a medium that lacks LEUKEMIC INHIBITORY FACTOR. The embryoid bodies can further differentiate into cells that represent different lineages.

Attributes by original data submitter

Sample

source_name
Embryoid body cells
differentiation stage
ES-derived embryoid bodies at day 5
strain
C57BL/6
genotype
Gcn5-/-
chip antibodies
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarifed from the sonicated nuclei of day 5 EBs, and chromatin fragments were isolated with antibodies indicated. ChIP libraries were prepared using a Kapa Hyper Preparation kit (KAPA Biosystems, Wilmington, MA) protocol for Illumina Platforms. Briefly, for each library, 5ng of ChIP DNA was end-repaired and 3’-adenylated using a proprietary master mix, then ligated to the specific NexTflex adaptors from Bioo Scientific (Bioo Scientific, Austin, TX). The adaptor-ligated DNA was enriched using a KAPA Hyper Library Preparation kit (KAPA Biosystems, KK8502) with 5 cycles of PCR (1 cycle at 98°C for 45 seconds; 4 cycles of 98°C for 15 seconds, 60°C for 30 seconds, and 72°C for 30 seconds; 1 cycle at 72°C for 1 minute), then purified with AmpureXP beads (Beckman Coulter, A63881). The library quality was validated on a 2200 TapeStation from Agilent Technologies (Agilent, Santa Clara, CA). Concentrations of the libraries were determined using a Kapa Library Quantification Kit (KAPA Biosystems, KK4933) and loaded on cBOT (Illumina) at final concentration of 1.5nM for cluster generation, then sequenced with 50bp single-read on a HiSeq3000 sequencer (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 3000

mm10

Number of total reads
35085151
Reads aligned (%)
94.5
Duplicates removed (%)
25.6
Number of peaks
528 (qval < 1E-05)

mm9

Number of total reads
35085151
Reads aligned (%)
94.2
Duplicates removed (%)
25.6
Number of peaks
585 (qval < 1E-05)

Base call quality data from DBCLS SRA