Curated Sample Data


Genome
dm3
Antigen Class
Input control
Antigen
Input control
Cell type Class
Embryo
Cell type
1-3h embryos

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
wt_input
genotype/variation
wild type
tissue
embryo
developmental stage
1-3 hours post egg laying
chip antibody
None

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Embryos (1-3 hours post egg laying) were collected with embryo wash (0.03% Triton-X100 and 140mM NaCl) and dechorionated in 100% bleach for 2 minutes. For each experiment, six aliquots each of 100ul of embryos were transferred to Eppendorf tubes containing 340ul of buffer A1 (15mM HEPES pH 7.5, 15mM NaCl, 60mM KCl, 4mM MgCl2, 0.5% Triton X-100, 0.5mM DDT, and complete EDTA-free protease inhibitor cocktail (Roche)). To each tube, 37% formaldehyde was added to a final concentration of 1.8%. Embryos were then homogenized with an Eppendorf micropestle and fixed on ice for 15’. Cross-linking was stopped by adding glycine to a final concentration of 0.125M. Homogenates were then centrifuged for 3’ at 3000 rpm in a microcentrifuge at 4°C. Supernatant was discarded and 340 ul buffer A1 was added to each tube. Pellets were suspended by vortexing and centrifuged two more times (three washes with buffer A1 in total), followed by two washes in 340ul buffer A2 (15mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 0.5mM EGTA, 1% Triton-X100, 0.1% sodium deoxycholate, 0.1% SDS, 0.5% N-lauroylsarcosine, complete EDTA-free protease inhibitor cocktail (Roche)). Pellets were then harvested by centrifuging at 14,000 rpm, snap-frozen in liquid nitrogen, and stored in -80°C for long-term storage. For each ChIP experiment, pellets were combined to yield 60 mg total, and sonicated in 200 ul buffer A2. Sonication was performed 4 times 30’’ on and 30’’ off with a Sonic Dismembrator Model 550 (Fisher Scientific) equipped with a microtip at power setting 3. Affymetrix/USB ChIP Assay Kits were used for immunoprecipitation. Libraries were made with NEXTflex™ ChIP-Seq Kit (BIOO Scientific, #5143-01) and barcoded with NEXTflex™ ChIP-seq Barcodes (BIOO Scientific, #514120).

Platform Information


instrument_model
Illumina HiSeq 2000

External Database Query

Logs in read processing pipeline


Number of total reads
9517831
Reads aligned (%)
98.5
Duplicates removed (%)
2.6
Number of peaks
1892 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA