Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Embryo
Cell type
Mixed embryo
NA
NA

Attributes by original data submitter

Sample

source_name
mixed-stage embryos
strain
GW0638
genotype
met-2(n4256) set-25(n5021) III
tissue
mixed-stage embryos

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Embryos were washed, dounced, and sheared as in Anderson et al 2019, except that no sarkosyl was added before shearing. Protein A Dynabeads (50 μL) (ThermoFisher Scientific, 10002D) were washed once in 1 mL FA buffer with protease inhibitors (150 mM NaCl, 50 mM HEPES-KOH pH 7.6, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 5 mM DTT, protease inhibitor cocktail, 1 mM PMSF). Beads were then incubated with 6.6 μg rat polyclonal anti-SDC-3 antibody (rb3779) for 90 min at room temperature in a total volume of 1 mL FA buffer plus protease inhibitors, and the supernatant was removed. Embryo extract containing approximately 2 mg of total protein was then added to the beads and incubated at room temperature for 90 min in a total volume of 1 mL FA buffer plus protease inhibitors. Beads were washed and DNA eluted as in Kruesi et al 2013. We performed end repair, A-tailing, ligation of NEXTflex DNA Barcodes, and amplification as in Kruesi et al 2013.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

ce11

Number of total reads
41859759
Reads aligned (%)
61.8
Duplicates removed (%)
31.8
Number of peaks
856 (qval < 1E-05)

ce10

Number of total reads
41859759
Reads aligned (%)
61.8
Duplicates removed (%)
31.8
Number of peaks
864 (qval < 1E-05)

Base call quality data from DBCLS SRA