Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
sdc-3

Cell type

Cell type Class
Embryo
Cell type
Mixed embryo
NA
NA

Attributes by original data submitter

Sample

source_name
whole worms
strain
ERC38
developmental stage
mixed embryo
antibody target
SDC-3
antibody antigen
1067-1340aa
matching input
SE365 input ERC38 MxEmb ChIP-seq

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Embryos were washed 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 embryo 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

ce10

Number of total reads
14706632
Reads aligned (%)
80.9
Duplicates removed (%)
10.5
Number of peaks
670 (qval < 1E-05)

ce11

Number of total reads
14706632
Reads aligned (%)
80.9
Duplicates removed (%)
10.5
Number of peaks
670 (qval < 1E-05)

Base call quality data from DBCLS SRA