Curated Sample Data


Genome
dm3
Antigen Class
Input control
Antigen
Input control
Cell type Class
Larvae
Cell type
Eye discs

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
ChIP_INPUTv_ED
strain
W1118 Oregon-R
develpmental stage
L3 wandering larvae
tissue
Eye Disc
chip antibody
No Ab

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP from ED or whole 14-16h embryos were performed in duplicate as previously described in Loubiere et al., 2016. Briefly, ~200 ED from wandering larvae were used per replicate for PTM ChIP-Seq and ~500 for PSC and SU(Z)12 ChIP-Seq. For each replicate of PTM ChIP-Seq from 14-16h embryos, 2h collections were performed at 25°C with about 500 flies. When necessary, several batches of dissection/collection were snap-frozen in liquid nitrogen and stored at -80°C in order to collect enough material. Samples were then transferred into a tight Tenbrock and cross-linked for 15min at RT using 1.8% formaldehyde and continuous homogenization before being lysed on ice for 2h with 1% SDS Lysis Buffer 2 (see Loubiere et al., 2016). Chromatin was sonicated using a Bioruptor (Diagenode) for 18 cycles (settings 30s ON, 30s OFF, high power) and the quality of the sonication was checked on a 1.5% agarose gel (~300bp fragments). Then, samples were pre-cleared O/N using 15µL of protein A Dynabeads (ThermoFisher Scientific, 10001D) at 4°C and an aliquot was kept apart to constitute the INPUT. Antibodies were added (see Supplementary Table 7) 4h prior to the addition of 30µL of protein A dynabeads and O/N incubation at 4°C. Finally, beads were washed, and the precipitated chromatin was eluted before O/N decrosslinking at 65°C, Proteinase K treatment, Phenol/Chloroform purification and O/N ethanol precipitation. Libraries were prepared using the TruSeq ChIP Sample Preparation kit from Illumina, following manufacturers' instructions.

Platform Information


instrument_model
Illumina HiSeq 2000

External Database Query

Logs in read processing pipeline


Number of total reads
50454880
Reads aligned (%)
92.6
Duplicates removed (%)
50.6
Number of peaks
9915 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA