Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ubx

Cell type

Cell type Class
Cell line
Cell type
Kc167
Source
e/se
Developmental Stage
dorsal closure stage

Attributes by original data submitter

Sample

source_name
anti-GFP ChIP DNA from Kc167 cells expressing Ubx-GFP and Hth (Experiment 2)
cell line
Kc167
cell line source
Female late embryo derived cell line
antibody
anti-GFP

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was prepared from FACS-sorted Hox-GFP expressing cells, and Hox-DNA complexes were immunopurified using anti-GFP antibody. Detailed protocol is described in associated publication. Samples were processed and sequenced by Source BioScience. The Illumina TruSeq ChIP Sample Preparation Kit was used to generate indexed paired-end sequencing libraries in accordance with the manufacturer’s guide (Rev. A, August 2012) except that no size selection was performed. For the ChIP samples, the entire 10 µl volume of ChIP DNA was used for library preparation and 17 cycles of amplification were performed. For the input sample, 5-10 ng of input DNA were used for library preparation and 12 cycles of amplification were performed. Samples were either sequenced on the Illumina MiSeq (Experiment 1; Ubx, Abd-A, Abd-B and input) or HiSeq 2000 (Experiment 2; Ubx, mutant Ubx and Ubx+Hth) platforms to generate 36 bp or 100 bp reads respectively.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

dm3

Number of total reads
90015801
Reads aligned (%)
36.2
Duplicates removed (%)
76.5
Number of peaks
15210 (qval < 1E-05)

dm6

Number of total reads
90015801
Reads aligned (%)
28.8
Duplicates removed (%)
80.6
Number of peaks
9736 (qval < 1E-05)

Base call quality data from DBCLS SRA