Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
dpy-27

Cell type

Cell type Class
Embryo
Cell type
Embryos
NA
NA

Attributes by original data submitter

Sample

source_name
whole worms
strain
CB428
developmental stage
embryo
matching input raw data file
Input_CB428_MxEmb_Rep3.fastq.gz
antibody
DPY-27 JL00001 Rabbit polyclonal to 1-409 aa. (Ercan et al. Nat Genet. 2007) is against the antigen 1-409 aa

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 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

ce10

Number of total reads
7648332
Reads aligned (%)
74.0
Duplicates removed (%)
14.5
Number of peaks
875 (qval < 1E-05)

ce11

Number of total reads
7648332
Reads aligned (%)
74.0
Duplicates removed (%)
14.5
Number of peaks
876 (qval < 1E-05)

Base call quality data from DBCLS SRA