Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Su(var)205

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
H1-KD OSC
cell type
Ovarian Somatic Cells (OSC)
variation
RNAi H1
chip antibody
anti-HP1a antibody (C1A9, DSHB)

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

dm3

Number of total reads
4878566
Reads aligned (%)
74.4
Duplicates removed (%)
5.4
Number of peaks
2637 (qval < 1E-05)

dm6

Number of total reads
4878566
Reads aligned (%)
73.3
Duplicates removed (%)
8.0
Number of peaks
2086 (qval < 1E-05)

Base call quality data from DBCLS SRA