Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
dwg

Cell type

Cell type Class
Embryo
Cell type
Embryos
NA
NA

Attributes by original data submitter

Sample

source_name
Embryo
strain
Oregon R
tissue
Embryo
chip antibody
Zw5 (rabbit, aa 98-302)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin for input (0.5 ug of DNA) was brought to RIPA conditions (140mM NaCl / 10mM Tris-HCl pH8,0 / 1mM EDTA / 1% TritonX100 / 0,1% SDS / 0,1% sodium deoxycholate, 1mM PMSF) was diluted in TE with 0.5% SDS, treated with RNase A for 30 min and protease K overnight, incubated at 65 degrees for 6 hours and phenol chloroform extracted. Sepharose was resuspended in TE with 0.5% SDS, treated with RNase A for 30 min and protease K overnight, incubated at 65 degrees for 6 hours and phenol chloroform extracted. To construct the libraries DNA was processed as described in the TruSeq RNA Sample Preparation Guide (Illumina) v2 from the end repair stage. This protocol has been chosen because of the very low amount of input DNA (<<10ng). Amplified libraries were quantified using fluorimetry with Qubit (Invitrogen, USA) and real-time PCR and diluted up to final concentration of 10 pM. Diluted libraries were clustered on a single read flowcell using cBot instrument and sequenced in 51 cycles using HiSeq2000 sequencer with TruSeq SBS Kit v3-HS (Illumina, USA). We sequenced an input sample as well as one sample for each of Pita, ZIPIC, Zw5 and preimmune chromatin immunoprecipitates.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

dm3

Number of total reads
11450650
Reads aligned (%)
87.6
Duplicates removed (%)
22.9
Number of peaks
1815 (qval < 1E-05)

dm6

Number of total reads
11450650
Reads aligned (%)
86.6
Duplicates removed (%)
26.8
Number of peaks
1588 (qval < 1E-05)

Base call quality data from DBCLS SRA