Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Clamp

Cell type

Cell type Class
Embryo
Cell type
Embryos
NA
NA

Attributes by original data submitter

Sample

source_name
sorted female-enriched embryos
nuclear cycle
12
chip antibody
CLAMP (3 μL of Novus/SDIX rabbit anti-CLAMP)
replicate
2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
To obtain female embryos, we mated +; SD72/CyO females to 19-3, yw, Rsp[s]-B[s]/Dp(2:y)CB25-4, y+, Rsp[s]B[s]; SPSD/CyO males (both kind gifts from Cynthia Staber) to obtain +/Dp(2:y) CB25-4, y+, Rsp[s]B[s]; SPSD/SD72 males, which we then mated to yw; attP2{ PCNA-EGFP} females (kind gift from Shelby Blythe). We performed 0- to 4-h timed lays and collected and fixed embry- os according to Blythe and Wieschaus (2015). We then hand- sorted embryos using a Zeiss Discovery.V8 microscope under GFP excitation using an X-CITE 120Q stereo light source. We pooled 200 (NC 11–14) to 400 (NC < 11) embryos and performed ChIP as in Blythe and Wieschaus (2015) using 3 μL of rabbit anti-CLAMP antibody per sample. We synthesized libraries using the NEBNext ChIP-seq kit (New England Biosystems) and se- quenced libraries on an Illumina HiSeq 2500 in 2×100-bp mode. We mapped CLAMP ChIP-seq reads to the custom histone locus genome (McKay et al. 2015), allowing only unique alignments by using Bowtie aligner (Langmead et al. 2009).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

dm3

Number of total reads
45471418
Reads aligned (%)
42.2
Duplicates removed (%)
78.8
Number of peaks
7872 (qval < 1E-05)

dm6

Number of total reads
45471418
Reads aligned (%)
41.9
Duplicates removed (%)
83.5
Number of peaks
4047 (qval < 1E-05)

Base call quality data from DBCLS SRA