Curated Sample Data


Genome
ce10
Antigen Class
TFs and others
Antigen
cec-3
Cell type Class
Adult
Cell type
Young adult

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
whole young adult worm lysates
developmental stage
young adult
antibody
EAP-1 antibody
genotype
spr-5
generation
G20

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin preparation was performed as described in (Stock et al., 2007) with some modifications. Strains were maintained at 16°C until the appropriate generation and then shifted to 25°C after birth. 50 µl packed young adult worms were subjected to five freeze/thaw cycles in liquid N2, and fixed in 1% formaldehyde in PBS (10 min, RT). During fixation, worms were dounced 100 times in a glass homogenizer. Fixation was stopped by addition of Glycine to 0.125M (5 min, RT). Worms were washed in cold PBS, before “swelling” buffer (25 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl and 0.1% NP-40) was added to lyse the cells (10 min, 4°C). After resuspension in “sonication” buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and 0.1% SDS), nuclei were sonicated using a Misonix 3000 (Amplitude 60; 25 cycles; 15s ‘on’, 45s ‘off’; 4°C). The resulting material was centrifuged twice (10 min, 4°C) at 14,000 rpm. Swelling and sonication buffers were supplemented with 5 mM NaF, 1 mM PMSF, and protease inhibitor cocktail (Roche). ChIP-seq libraries were prepared using NEBNext DNA library preparation reagents (E6000) and the protocol and reagents concentrations described in the Illumina Multiplex ChIP-seq DNA sample Prep Kit. Libraries were indexed using a single indexed PCR primer. After PCR amplification, 300-600 bp DNA fragments were selected on an agarose gel. Libraries were quantified by Qubit (Invitrogen), and library size was assessed by Bioanalyzer (Agilent). Libraries were sequenced using a HiSeq 2000 (Illumina) to generate 50 bp single end reads. ChIP-seq libraries were generated from two biological repeats for G0 and G20, a single repeat for G10, and four Input samples.

Platform Information


instrument_model
Illumina HiSeq 2000

External Database Query

Logs in read processing pipeline


Number of total reads
20161513
Reads aligned (%)
40.8
Duplicates removed (%)
42.2
Number of peaks
561 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA