Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3

Cell type

Cell type Class
Adult
Cell type
Whole worm
NA
NA

Attributes by original data submitter

Sample

source_name
whole animal
strain
glp-1(e2141)
chip-antibody
H3
antibody source
H3 (ab1791, Abcam)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Adult worms at day 2, day 4 and day 12 stages were washed with ice cold M9 three times. Worm pellets were stored at -80°C before chromatin immunoprecipitation and RNA extraction. For ChIP-seq, chromatin immunoprecipitation was performed as described (Ercan et al. 2007; Landt et al. 2012). Worm pellet was grinded with mortar/pestle and cross-linked with 1% formaldehyde in PBS at room temperature for 10 min. Worm fragments were collected by spinning at 3,000 g for 5 min and resuspended in FA buffer followed by sonication with Bioruptor. For mRNA-seq, total RNA was extracted from worms harvested at the same stages as ChIP-seq sample preparation for glp-1(e2141), met-1(n4337); glp-1(e2141), or RNAi treated glp-1(e2141) worms. mRNA was purified through poly A enrichment and mRNA-seq before library preparation. For ChIP-seq,chromatin immunoprecipitation was performed as described (Ercan et al. 2007; Landt et al. 2012). Chromatin extract was incubated with H3 antibody (Rabbit, ab1791, Abcam), H3K36me3 antibody (Rabbit, ab9050, Abcam), and control rabbit IgG overnight at 4°C. Antibodies used were prescreened for specificity using dot blots. The optimal amounts of antibodies used were determined by titration in preliminary experiment with ChIP-qPCR. 10-15 ng precipitated DNA from each sample was used for illumina sequencing library preparation. DNA from ChIP was first end-repaired to generate blunt end, followed by adding single adenine base for adaptor ligation. Ligation product with adaptor was size selected and amplified by PCR with primers targeting adaptor. For mRNA-seq, mRNA was purified through poly A enrichment and mRNA-seq library was prepared with Illumina Truseq RNA and DNA sample prep kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

ce11

Number of total reads
8671434
Reads aligned (%)
89.6
Duplicates removed (%)
15.2
Number of peaks
3907 (qval < 1E-05)

ce10

Number of total reads
8671434
Reads aligned (%)
89.6
Duplicates removed (%)
15.2
Number of peaks
3909 (qval < 1E-05)

Base call quality data from DBCLS SRA