Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ama-1

Cell type

Cell type Class
Embryo
Cell type
Mixed embryo
NA
NA

Attributes by original data submitter

Sample

source_name
Mixed-stage embryos
strain
N2
treatment
Empty vector RNAi
chip antibody
SDQ2357_AMA1 [Novus Biologicals, catalog# 38520002, lot# G3048-029, Animal SDQ2357]

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The C. elegans N2 strain mixed-stage embryos were cross-linked in 2% formaldehyde for 30 min at 25ºC. Chromatin extract was prepared by sonication in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl). Five to ten micrograms of antibodies were immobilized on sepharose beads and incubated with the chromatin extract for >12 hours at 4ºC. After washing the immunoprecipitants followed by RNase treatment and reverse-crosslinking, DNA were extracted and purified. DNA was blunt-ended and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end primers. Amplicon was loaded on an agarose gel, and DNA at 200-500 bp was recovered from the gel.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

ce10

Number of total reads
10834267
Reads aligned (%)
45.4
Duplicates removed (%)
50.3
Number of peaks
3178 (qval < 1E-05)

ce11

Number of total reads
10834267
Reads aligned (%)
45.4
Duplicates removed (%)
50.3
Number of peaks
3181 (qval < 1E-05)

Base call quality data from DBCLS SRA