Curated Sample Data


Genome
ce10
Antigen Class
Histone
Antigen
H3K9me3
Cell type Class
Larvae
Cell type
L3

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
L3 larvae
strain
drh-3(ne4253)
antibody
H3K9me3(Abcam, ab8898)

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation was performed following the modENCODE Protocol from the Lieb Lab (modENCODE Consortium et al., 2009) with some modifications. The worm pellet fixed with 2% PFA for 30 minutes at 20°C was washed in M9 3 times and resuspended in RIPA buffer supplemented with Protease inhibitors (Thermo Scientific, 78443). DNA fragmentation was performed using sonication with Covaris (Peak power 240, Duty factor 20, Cycles/burst 200, 8 min). Then, 1.5–2mg of cross-linked chromatin extract was incubated at 4°C ON with a specific antibody and the immune complexes were then incubated with 50 µl IgG Dynabeads (Invitrogen) for 3h at 4°C. DNA was cleaned up with the Qiagen PCR purification kit. ChIP-seq libraries were prepared using TruSeq Illumina kit (set A – 15034288, set B - 15034289) according to manufacturer's instructions. Sequencing was performed on Illumina NextSeq500. The 75-bp single-end Illumina sequencing reads were preprocessed by trimming the adapter sequences with Cutadapt (Didion et al., 2017). After that, reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie for Illumina (Galaxy Version 1.1.2) (Langmead et al., 2009) with default settings. The SAMtools (Galaxy Version 1.1.2) (Li et al., 2009; Li, 2011) utility was used to convert the alignments to BAM format. A table containing the number of reads aligned to genome is included in supplementary data (Table 1).

Platform Information


instrument_model
NextSeq 500

External Database Query

Logs in read processing pipeline


Number of total reads
21298561
Reads aligned (%)
96.2
Duplicates removed (%)
19.4
Number of peaks
942 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA