Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
cuff

Cell type

Cell type Class
Adult
Cell type
Ovary
NA
NA

Attributes by original data submitter

Sample

source_name
ovary
tissue
ovary
genotype
wt
age
2-4 days
target
Cuff

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA-seq and ChIP-seq assays were performed in triplicate and for each biological replicate we dissected ovaries from approximately 30 female flies (2-4 days old). Total RNA was extracted using Trizol reagents (Life Technologies) and treated with turbo DNase-free kit (Ambion) to eliminate traces. of genomic DNA. DNA-free total RNA was subjected to two rounds of rRNA depletion using the Ribo-Zero rRNA removal kit (Epicentre) as per the manufacturer's instructions. The same ChIP protocol was employed for the ChIP-seq assays as previously described (Pane et al. 2011; Blythe et al. 2009). The Cuff-EGFP expressing transgenic line, GFP antibodies and the conditions used for the Cuff ChIP-seq experiment were previously described (Pane et al. 2011; Blythe et al. 2009). The RNA-seq library preparation was obtained with the ScriptSeq v2 kit (Epicentre) and the libraries were sequenced on the Illumina platforms. Chromatin fragments were used to generate DNA libraries with the ChIP-seq DNA Sample Prep kit (Illumina).

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

dm3

Number of total reads
51690992
Reads aligned (%)
6.5
Duplicates removed (%)
90.0
Number of peaks
3873 (qval < 1E-05)

dm6

Number of total reads
51690992
Reads aligned (%)
5.6
Duplicates removed (%)
91.3
Number of peaks
2740 (qval < 1E-05)

Base call quality data from DBCLS SRA