Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
hda-1

Cell type

Cell type Class
Embryo
Cell type
Mixed embryo
NA
NA

Attributes by original data submitter

Sample

source_name
Mixed Embryos
tissue
whole larvae
strain
cfp-1(tm6369)
Stage
MxE
chip antibody
anti-HDA1
chip antibody supplier
Novus Biologicals

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitations and library preparations were conducted as in (McMurchy et al., 2017), using formaldehyde as a fixitive for the H3K4me3 ChIPs (30ug DNA, 2.5ug antibody) and formaldehyde and EGS as fixatives for the SIN-3 (15ug DNA, 2.5ug antibody) and HDA-1 (30ug DNA, 2.5ug antibody) ChIPs. Approximately 10% C. briggsae chromatin extract was spiked into the C. elegans extract for the H3K4me3 ChIPs and 5% into the HDA-1 ChIPs. The HDA-1 antibody did not detect C. briggsae HDA-1 and so was not used for normalization.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

ce10

Number of total reads
19402523
Reads aligned (%)
81.9
Duplicates removed (%)
13.8
Number of peaks
7037 (qval < 1E-05)

ce11

Number of total reads
19402523
Reads aligned (%)
81.9
Duplicates removed (%)
13.8
Number of peaks
7148 (qval < 1E-05)

Base call quality data from DBCLS SRA