Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Embryo
Cell type
Embryos
NA
NA

Attributes by original data submitter

Sample

source_name
late C. elegans embryos N2
tissue
whole embryo
genotype
N2 wild type

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Embryos were fixed with 2% formaldehyde for 30 min and quenched with 0.1 M Tris pH7.5. Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction antibody was first incubated overnight at 4 C then Protein A agarose beads were incubated overnight at 4 C. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by Qiaquick (Qiagen) extraction. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

Sequencing Platform

instrument_model
NextSeq 500

ce11

Number of total reads
17696870
Reads aligned (%)
87.8
Duplicates removed (%)
26.2
Number of peaks
4878 (qval < 1E-05)

ce10

Number of total reads
17696870
Reads aligned (%)
87.8
Duplicates removed (%)
26.2
Number of peaks
4879 (qval < 1E-05)

Base call quality data from DBCLS SRA