Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GFP

Cell type

Cell type Class
Embryo
Cell type
Mitotic cycle 13
NA
NA

Attributes by original data submitter

Sample

source_name
embryo
developmental stage
NC13
maternal genotype
zld[294]; RpA-70-EGFP/+
chip antibody
anti-Green Fluorescent Protein, millipore ab3080

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
150 embryos (NC12 and NC13) or 100 embryos (NC14 E, M, or L) were hand selected on the basis of nuclear morphology and density following 15’ cross linking in 1% formaldehyde/Heptane/PBS/0.5% Triton X-100. Samples were homogenized in 1% RIPA buffer plus protease and phosphatase inhibitors and 1mM DTT. Cleared nuclear pellets were sonicated for 7x 20 seconds to shear chromatin to ~300 bp average size followed by overnight immunoprecipitation and 1h complex capture on Protein G dynabeads. Following two low and high salt washes, purified complexes were eluted, RNase treated, and cross links were reversed in the presence of Proteinase K. DNA was purified via Qiagen spin column. NEBNext ChIP Seq library master mix kit for Illumina was used according to the manufacturer’s specifications, using 1 ng input chromatin or the entire ChIP sample for library preparation. Ampure beads were used for size-selection prior to PCR amplification with barcoding primers. Mean library fragment size was ~270 bp. Libraries were sequenced on an Illumina HiSeq 2500 with read length of 67 bp except for mei-41 samples which were sequenced at 141 bp.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

dm6

Number of total reads
75723301
Reads aligned (%)
93.8
Duplicates removed (%)
81.7
Number of peaks
8333 (qval < 1E-05)

dm3

Number of total reads
75723301
Reads aligned (%)
94.5
Duplicates removed (%)
76.2
Number of peaks
14212 (qval < 1E-05)

Base call quality data from DBCLS SRA