Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H2AvD

Cell type

Cell type Class
Cell line
Cell type
S2
Source
Oregon R
Developmental Stage
late embryonic stage

Attributes by original data submitter

Sample

source_name
S2 cell line
cell line
S2 cells
treatment
GAF-RNAi
chip antibody
Anti-H2AvD antisera (Glaser lab stock)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Ten million cross-linked nuclei were digested with MNase until about 80% of the material has mononucleosome-sized. For H2AvD nucleosomes, immunoprecipitated with 4ul Anti-H2AvD antisera (Glaser lab stock) from 75ul of digested material. Cross-links were reversed at 65°C and the DNA was extracted with phenol:chloroform and precipitated. 50ng of non-immunoprecipitated (MNase-seq) or immunoprecipitated (H2AvD) DNA was ligated to Tru-seq paired-end adapters. The resulting DNA was PCR amplified for 5 cycles and 200-400bp fragments were selected and PCR amplified for 12-15 cycles. The cDNA was then paired-end sequencing was performed (50 bases) on the Illumina HiSeq 2500.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

dm6

Number of total reads
8710535
Reads aligned (%)
86.9
Duplicates removed (%)
3.5
Number of peaks
818 (qval < 1E-05)

dm3

Number of total reads
8710535
Reads aligned (%)
87.2
Duplicates removed (%)
2.9
Number of peaks
1691 (qval < 1E-05)

Base call quality data from DBCLS SRA