Curated Sample Data


Genome
dm3
Antigen Class
Input control
Antigen
Input control
Cell type Class
Cell line
Cell type
S2

Cell type information


Source
Oregon R
Developmental Stage
late embryonic stage

Attributes by Original Data Submitter


source_name
S2 cells
cell line
S2
gender
male
chip antibody
none

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
H3K36me3 ChIP-seq was performed on MNase digested chromatin as described previously (Straub et al., 2008 and Kasinathan et al., 2013) with some modifications. Cells were fixed in 1% formaldehyde for 1 min at 26°C, followed by quenching with 125 mM glycine and washing with PBS. Nuclei were released by resuspending in TM2+ with NP-40. MNase digestion was performed in TM2+IC using 4U MNase (Sigma Aldrich, resuspended in EX50 (Bonte & Becker, 1999)) in the presence of CaCl2 for 13 min at 37 °C. Reaction was stopped with EGTA and Triton-X-100, SDS, NaDOC and NaCl was added to final concentration as in RIPA Buffer. MNase digested chromatin was incubated for 1 h at 4°C while slight agitation and chromatin was solubilized by passing ten times through 27 G needle and centrifuged for 30 min at 15,000 g at 4°C. ChIP was performed from soluble chromatin using H3K36me3 antibody (ab9050, Abcam).

Platform Information


instrument_model
Illumina HiSeq 1500

External Database Query

Logs in read processing pipeline


Number of total reads
14188970
Reads aligned (%)
98.2
Duplicates removed (%)
20.0
Number of peaks
2383 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA