Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
bcd

Cell type

Cell type Class
Embryo
Cell type
Embryos
NA
NA

Attributes by original data submitter

Sample

source_name
wild-type (graded) Bcd Chromatin Immunoprecipitation
timepoint
NC14
tissue
embryo
number of embryos
200

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Embryos from a 0-4 hour collection were crosslinked in formaldehyde for 15 minutes prior to quenching with glycine and 3 1x PBS washes. Embryos were hand sorted under a dissecting scope in order to collect NC14 stage only. Collected embryos were frozen at -80° until sufficient numbers were collected. To perform ChIP, collected embryos were thawed and homogenized prior to sonication in RIPA buffer. Sheared chromatin was subjected to overnight immunoprecipitation with an anti-GFP antibody and immunocomplexes were precipitated with protein-G dynambeads. Pellets were washed extensively prior to elution and crosslink reversal. ChIP samples were subjected to library preparation using the NEB Next Library Mastermix Kit following the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

dm3

Number of total reads
18118335
Reads aligned (%)
48.9
Duplicates removed (%)
32.6
Number of peaks
2105 (qval < 1E-05)

dm6

Number of total reads
18118335
Reads aligned (%)
46.2
Duplicates removed (%)
35.8
Number of peaks
2500 (qval < 1E-05)

Base call quality data from DBCLS SRA