Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
lem-2

Cell type

Cell type Class
Embryo
Cell type
Early embryo
NA
NA

Attributes by original data submitter

Sample

source_name
Early embryo extracts
developmental stage
early embryo
strain
GW828
genotype/variation
cec-4_delta
chip antibody
anti-LEM-2 (Novus Biologicals, catalog #48540002, lot# T01872A01)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
LEM-2 ChIP was performed as described in (Ikegami et al., 2010) with anti-LEM-2 (Novus Biologicals #48540002) Libraries were prepared from chromatin IP (1.7 -7.4 ng) and input (10 ng) samples using the NEBNext ultra DNA library prep kit for Illumina (NEB # 7370) and the NEBNext Multiplex Oligos for Illumina (NEB # E7335), according to the manufacturer’s recommendations. No size selection was performed during sample preparation and the libraries were indexed and amplified using 15 PCR cycles, using the recommended conditions. After a final cleanup with Agencourt AmPure XP beads (Beckman # A63881), the library size distribution and concentrations were determined using a BioAnalyzer 2100 (Agilent technologies) and Qubit (Invitrogen) instrument, respectively. The final pools were prepared by mixing equimolar amounts of all individual indexed libraries and then sequenced on a HiSeq 2500 (Illumina) in Rapid mode (Paired-End 50).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

ce10

Number of total reads
14864045
Reads aligned (%)
191.9
Duplicates removed (%)
1.6
Number of peaks
891 (qval < 1E-05)

ce11

Number of total reads
14864045
Reads aligned (%)
191.9
Duplicates removed (%)
1.6
Number of peaks
892 (qval < 1E-05)

Base call quality data from DBCLS SRA