Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
sdc-3

Cell type

Cell type Class
Embryo
Cell type
Mixed embryo
NA
NA

Attributes by original data submitter

Sample

source_name
mixed-stage embryos
strain name
TY5867
genotype
yIs196(rex-14) yIs190(rex-47) yIs192(rex-8) I; rex-14(y738) rex-47(y671) rex-8(y737) X
antibody
anti-SDC-3

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Embryos were ground with 50 strokes in a 2 mL dounce homogenizer. Sarkosyl was added to a final concentration of 0.1% and chromatin was sheared in an S2 Covaris with duty cycle 20%, intensity 8, and 200 cycles/burst for 30 cycles of 60 sec with 45 sec of rest for a total time of 52 min. The extract was centrifuged at maximum speed for 15 min at 4° C. Supernatant containing approximately 2 mg total protein was incubated with 6.6 μg rabbit polyclonal anti-DPY-27 (rb699) (Chuang et al., 1994), rat polyclonal anti-SDC-3 (PEM4A) (Crane et al., 2015), or random IgG antibodies overnight at 4° C in a volume of at least 500 μl. 50 μl of Protein A Dynabeads (ThermoFisher Scientific, 10002D) were washed in FA buffer three times, added to the immunoprecipitation, and mixed at 4° C for at least 2 hr. Beads were then 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

ce10

Number of total reads
43368755
Reads aligned (%)
52.9
Duplicates removed (%)
28.2
Number of peaks
948 (qval < 1E-05)

ce11

Number of total reads
43368755
Reads aligned (%)
52.9
Duplicates removed (%)
28.2
Number of peaks
932 (qval < 1E-05)

Base call quality data from DBCLS SRA