Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
No description
Cell type
NA
NA
NA

Attributes by original data submitter

Sample


Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were harvested and fixed using 1% formaldehyde in PBS for 10 min at 23°C in an Eppendorf Thermomixer at 700 rpm, then sorted using a MoFlo FACS machine (Beckman Coulter) to standardise levels of Hox-GFP proteins across experiments, and finally sonicated to provide chromatin fragments of approximately 500 bp in length. Fragmented chromatin was immunoprecipitated using an anti-GFP antibody (SIGMA, G1544) and DNA was purified using a standard phenol-chloroform extraction. Sequencing libraries were prepared using the SMARTer ThruPLEX DNA-seq Kit (Takara Bio Inc.) in accordance with the sample preparation guide.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

dm6

Number of total reads
54438852
Reads aligned (%)
87.1
Duplicates removed (%)
47.8
Number of peaks
4454 (qval < 1E-05)

dm3

Number of total reads
54438852
Reads aligned (%)
92.1
Duplicates removed (%)
46.8
Number of peaks
6761 (qval < 1E-05)

Base call quality data from DBCLS SRA