Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ama-1

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
Input_CB428_MxEmb_Rep3.fastq.gz
antibody
AMA1 Q2357 Rabbit polyclonal is against the antigen DLVLDVEKCKYGMEIPQNVVMGGGFYGSFAGSPSNREFSPAHSPWNSGVTPTYAGAAWSPTTGGMSPGAGFSPAGNTDGGASPFNEGGWSPASPGDPLGA May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"

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

ce11

Number of total reads
9521857
Reads aligned (%)
82.1
Duplicates removed (%)
18.4
Number of peaks
2691 (qval < 1E-05)

ce10

Number of total reads
9521857
Reads aligned (%)
82.1
Duplicates removed (%)
18.4
Number of peaks
2710 (qval < 1E-05)

Base call quality data from DBCLS SRA