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
N2
developmental stage
L3
antibody
None (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Frozen Larva were broken into pieces using cryo-mixer mill, and crosslinked with 1% formaldehyde for 10 minutes. The worms were collected by centrifugation, were washed with and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of larva extract and 3-5 ug of antibody was used per ChIP. Half of the ChIP DNA were ligated to Illumina or home-made 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
19590984
Reads aligned (%)
95.2
Duplicates removed (%)
26.5
Number of peaks
0 (qval < 1E-05)

ce10

Number of total reads
19590984
Reads aligned (%)
95.2
Duplicates removed (%)
26.5
Number of peaks
0 (qval < 1E-05)

Base call quality data from DBCLS SRA