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
treatment
jil-1_1 RNAi
chip antibody
none

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq on MNase-digested chromatin in combination with mild sonication, S2 cells (~3 * 10^8 cells) after RNAi treatment were cross‑linked with 1% formaldehyde for 8 min at room temperature and the reaction was stopped by adding glycine. 5% 79f7Dv3 cells, processed as described for S2 cells without RNAi treatment, relative to S2 cells were added. Isolated nuclei were resuspended in RIPA (10 mM Tris/HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% (v/v) Triton‑X 100, 0.1%(v/v) SDS, 0.1% (v/v) DOC) supplemented with PI and 2 mM CaCl2 at 7 * 10^7 cells/mL and digested in 1 mL aliquots by adding 0.6 U MNase (Sigma Aldrich), resuspended in EX50 at 0.6 U/µL (Bonte and Becker, 1999), and incubating at 37°C for 35 min with slight agitation. The reaction was stopped by adding 10 mM EGTA and placing on ice. Digested chromatin was sheared with Covaris AFA S220 using 12x12 tubes at 50 W peak incident power, 20% duty factor and 200 cycles per burst for 8 min at 5°C. Subsequent steps were performed as described in (Albig et al., 2019). In brief, 100 µL soluble chromatin was pre‑cleared with 3 µL (6 µL 50% slurry) Protein A:Protein G (1:1) beads (GE Healthcare) and supernatant was directly used for immunoprecipitation by adding antibody to 300 µL chromatin adjusted to 500 µL with RIPA and incubated for 16 h at 4°C. 100 µL supernatant was added to 3 µL (6 µL 50% slurry) Protein A:Protein G beads (1:1) and incubated for 4 h at 4°C. Beads were washed five times with RIPA. For DNA recovery, beads were resuspended in 6.7 bed volumes TE Buffer (10 mM Tris/HCl pH 8.0, 1 mM EDTA), RNA was digested with 50 µg/mL RNaseA (Sigma‑Aldrich) for 30 min at 37°C, and protein was digested with 0.5 µg/mL Proteinase K (Sigma‑Aldrich) supplemented with 0.5% (v/v) SDS for 16 h at 65°C. DNA was purified with 1.8x AMPure XP beads (Beckmann Coulter). Libraries were prepared with NEBNext ChIP‑Seq Library Perp Kit for Illumina (NEB).

Platform Information


instrument_model
Illumina HiSeq 1500

External Database Query

Logs in read processing pipeline


Number of total reads
16143653
Reads aligned (%)
89.0
Duplicates removed (%)
19.0
Number of peaks
1968 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA