Curated Sample Data


Genome
dm3
Antigen Class
Histone
Antigen
H2Bub
Cell type Class
Embryo
Cell type
1-3h embryos

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
1-3 hr embryo
tissue
1-3 hr embryo
genotype
wild type
replicate
1749_2
ip target
ubH2B
antibody
mouse α-ubH2B (17-650)
epitope
Lys120 ubiquitination site

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Embryos were fixed in 1.8% formaldehyde for 15 min at room temperature. Cross-linking was stopped by addition of glycine to a final concentration of 125 mM. Embryos were homogenized in buffer A1 (15 mM HEPES at pH 7.5, 15 mM NaCl, 60 mM KCl, 4 mM MgCl2, 0.5% TritonX-100, 0.5 mM DTT) (0.1g embryos/1ml A1). The chromatin pellet was washed three times with 5ml buffer A1 and once with 5ml buffer A2 (15 mM HEPES at pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% TritonX-100, 0.1% sodium deoxycholate, 0.1% SDS, 0.5% N-lauroyl sarcosine). The chromatin was sonicated in 250μL of buffer A2 (0.1g embryos/250ul A2) seven times for 10 sec (0.9s on/0.1s off for 10 times) at 30% power. After centrifugation at 14,000 rpm for 10 min at 4°C, 250 μL of clarified soluble chromatin was used for ChIP as described previously (Huang et al. 2014). The antibodies used for ChIP included 10 μg of rabbit α-Sgf11, 20 μg of rabbit α-Ada2b, 20 μg of rabbit α-Spt3, 20 μg of rabbit α-Non-stop, 3 μg mouse α-pol2(4H8) (ab5408, Abcam). For ChIP-seq library preparation, 10ng ChIP DNA and WCE DNA were used with the KAPA HTP Library Prep Kit for Illumina and Bioo Scientific NEXTflex DNA barcodes. The resulting libraries were purified using the Agencourt AMPure XP system (Beckman Coulter) then quantified using a Bioanalyzer (Agilent Technologies) and a Qubit fluorometer (Life Technologies). Post amplification size selection was performed on all libraries using a Pippin Prep (Sage Science). Libraries were re-quantified, normalized, pooled and sequenced on an Illumina HiSeq 2500 instrument as 50-bp single read.

Platform Information


instrument_model
Illumina HiSeq 2500

External Database Query

Logs in read processing pipeline


Number of total reads
28358405
Reads aligned (%)
83.1
Duplicates removed (%)
18.7
Number of peaks
6529 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA