Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Larvae
Cell type
L3
NA
NA

Attributes by original data submitter

Sample

source_name
whole worms
strain
CB428
developmental stage
L3
antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Frozen, ground, and crosslinked larva samples were resuspended in FA buffer+sarkosyl+protease inhibitors (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl, 0.1% sarkosyl), and sonicated to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of extract was spiked in with 0.1-0.2 mg of C. Briggsae AF16 extract and 3-5 ug of antibody was used per ChIP. Half of the ChIP DNA and 10-20 ng of input DNA were ligated to Illumina multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

ce11

Number of total reads
13951354
Reads aligned (%)
88.1
Duplicates removed (%)
7.5
Number of peaks
646 (qval < 1E-05)

ce10

Number of total reads
13951354
Reads aligned (%)
88.1
Duplicates removed (%)
7.5
Number of peaks
639 (qval < 1E-05)

Base call quality data from DBCLS SRA