Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Cell line
Cell type
OSC
Tissue Source
ovary
Developmental Stage
adult stage

Attributes by original data submitter

Sample

source_name
Control-KD OSC
cell type
Ovarian Somatic Cells (OSC)
variation
RNAi EGFP

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
OSC cells were fixed, lysed, and their nuclei isolated using truChIP Chromatin Shearing Kits (Covaris) according to the manufacturer's instructions. DNA was sonicated to ~300 bases using Bioruptor (Cosmobio), then diluted with ChIP buffer. IP was performed using 3 μg of antibodies on Dynabeads-Protein G beads. Samples were reverse cross-linked, treated with RNase and Proteinase K, and DNA was extracted. DNA fragments from the ChIP experiment were sheared to ~200 bases using Covaris S220 (Covaris), and were used for library preparation with the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) following the manufacturer's protocol.

Sequencing Platform

instrument_model
Illumina MiSeq

dm6

Number of total reads
5615224
Reads aligned (%)
79.2
Duplicates removed (%)
4.8
Number of peaks
1296 (qval < 1E-05)

dm3

Number of total reads
5615224
Reads aligned (%)
80.0
Duplicates removed (%)
3.5
Number of peaks
568 (qval < 1E-05)

Base call quality data from DBCLS SRA