Curated Sample Data


Genome
ce10
Antigen Class
TFs and others
Antigen
lir-3
Cell type Class
Unclassified
Cell type
Unclassified

Cell type information


NA
NA

Attributes by Original Data Submitter


Sample Name
source LIR3_Rep1

Metadata from Sequence Read Archive

Library Description


library_name
LIR3_Rep1
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Worm staging was achieved by bleaching and L1 starvation. Arrested L1 animals were plated on peptone-enriched NGM plates seeded with OP50 bacteria and grown for 48 hours for L4 collection at 20C. Samples were crosslinked with 2% formaldehyde for 30 minutes at room temperature and then quenched with 1 M Tris pH 7.5. The pelleted worms were subsequently flash frozen in liquid nitrogen and stored at -80C. Samples were sonicated using a microtip to obtain mostly 200 to 800 bp DNA fragments. For each sample, 2.2 or 4.4 mg of cell extract was immunoprecipitated using a goat anti-GFP, GoatV (gift from Kevin White). The enriched DNA fragments and input control (genomic DNA from the same sample) for two biological replicates were used for library preparation and sequencing as previously described (Kasper et al., 2014). Briefly, samples were libraried and multiplexed using the Ovation Ultralow DR Multiplex Systems 1-8 and 9-16 (NuGEN Technologies Inc., San Carlos, CA) following the manufacturers protocol except Qiagen MinElute PCR purification kits were used to isolate the DNA. Library size selection in the 200-800 bp range was achieved using the SPRIselect reagent kit (Beckman Coulter, Inc., Brea, CA

Platform Information


instrument_model
Illumina HiSeq 2000

External Database Query

Logs in read processing pipeline


Number of total reads
12430706
Reads aligned (%)
91.4
Duplicates removed (%)
17.4
Number of peaks
818 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA