Curated Sample Data


Genome
dm3
Antigen Class
Input control
Antigen
Input control
Cell type Class
Adult
Cell type
Testis

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
whole testes
stock
w1118
developmental stage
adult
tissue
whole testes
chip antibody
none

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
2000 testes from w1118 males were dissected and fixed (see Materials and Methods section for details). Fixed testes were stored at 4°C in wash B. Testes were hand-dissected in wash B to remove the accessory glands. Pools of 1000 testes were transferred in 700ul of sonication buffer dissected in wash B to remove the accessory glands. Pools of 1000 testes were transferred in 700ml of sonication buffer. Conditions were established to obtain chromatin fragments 200-500 bp in length. ChIP-seq, library construction, cluster generation and Sequencing analysis were performed using the Illumina HiSeq2000, sequencing type SR50, following manufacture's protocols (www.illumina.com). In brief, libraries were prepared using Illumina's ChIP-Seq Sample Prep Kit from 3.5 ng of ChIP/Input DNA. Samples were size selected to ̴300-350 bp using DNA magnetic beads. Adaptor-modified DNA fragments were subjected to limited PCR amplification (18 cycles). Using Illumina's Cluster Generation Kit, libraries were subject to cluster generation for subsequent sequencing.

Platform Information


instrument_model
Illumina Genome Analyzer IIx

External Database Query

Logs in read processing pipeline


Number of total reads
22425200
Reads aligned (%)
84.8
Duplicates removed (%)
35.0
Number of peaks
1797 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA