Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Larvae
Cell type
L4
NA
NA

Attributes by original data submitter

Sample

source_name
Whole worm
developmental stage
L4
genotype
Wild type

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
L4 stage worms were collected at 20°C. The worms were crosslinked with 1x linking buffer (11 mM HEPES-NaOH, 110 mM NaCl, 1.1 mM EDTA and 1.1 mM EGTA) with 1% formaldehyde for 10 minutes at RT. The reaction was quenched by adding glycine to 0.125 M final concentration for 5 minutes at RT. Samples were washed with cold PBS twice. The samples were next dissociated with lysis buffer and sonicated by biorupter for 25 cycles in the cold room with 30 seconds on and 30 seconds off per cycle. Protein G beads were coupled to the flag antibody (F3165 Sigma) for 2 hours. Uncoupled Protein G beads were incubated with the sonicated samples to pull down non-specific binding chromatin. The precleared chromatin samples were incubated with antibody-coupled bead slurries and rotated at 4°C overnight. The bound DNA was eluted from the beads by 200 µl TE with 1% SDS after washing with low salt (0.2% SDS, 2% Triton X-100, 4 mM EDTA, 40 mM Tris-HCl), high salt (0.2% SDS, 2% Triton X-100, 4 mM EDTA, 40 mM Tris-HCl, and 1 M NaCl) and LiCl buffers (0.5 M LiCl, 2% NP-40, 1% Na deoxycholate, 2 mM EDTA, and 20 mM and Tris-HCl). The eluted DNA was next purified by phenol-chloroform. NEBNext DNA library prep master mix set for Illumina (E6040L) was used follow the companies instructions.

Sequencing Platform

instrument_model
NextSeq 500

ce11

Number of total reads
12139418
Reads aligned (%)
68.4
Duplicates removed (%)
19.5
Number of peaks
433 (qval < 1E-05)

ce10

Number of total reads
12139418
Reads aligned (%)
68.4
Duplicates removed (%)
19.5
Number of peaks
435 (qval < 1E-05)

Base call quality data from DBCLS SRA