Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
grh

Cell type

Cell type Class
Embryo
Cell type
15-16h embryos
NA
NA

Attributes by original data submitter

Sample

source_name
embryo
strain
wild type
antibody
GRH
Stage
15-16 hours after egg laying

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: Embryos were collected, fixed in formaldehyde, chromatin was isolated, and the chromatin was immunoprecipitated as described in Li et al., 2008. Immunoprecipitation was done using two antibodies against Grainy head and an input sample was also collected for sequencing. RNA-seq: Embryos depleted of either maternal or zygotic GRH as well as sibling controls were collected and examined to determine the stage. 7 embryos were collected for each set and lysed in TRIzol reagent (Life Technologies) supplemented with 150 µg/ml glycogen. RNA was extracted and cDNA libraries were prepared using the Illumina Truseq RNA sample prep kit. ChIP-seq libraries were prepared using standard Illumina protocols and RNA-seq libraries were prepared using Illumina Truseq RNA sample prep kit according to manufacterer's instructions

Sequencing Platform

instrument_model
Illumina HiSeq 2000

dm3

Number of total reads
29339865
Reads aligned (%)
75.0
Duplicates removed (%)
20.0
Number of peaks
10887 (qval < 1E-05)

dm6

Number of total reads
29339865
Reads aligned (%)
73.5
Duplicates removed (%)
21.3
Number of peaks
11825 (qval < 1E-05)

Base call quality data from DBCLS SRA