Curated Sample Data


Genome
dm3
Antigen Class
Input control
Antigen
Input control
Cell type Class
Embryo
Cell type
12-24h embryos

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
Developmental Stage Embryo 12-24h
tissue
Developmental Stage Embryo 12-24h
developmental stage
Embryo 12-24h
antibody
none
genotype
wildtype

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
We followed the BioTAP-XL protocol as described in (Alekseyenko et al. 2015). In brief, 12-24 hr old embryos from transgenic fly lines expressing BioTAP-N-Br140 were collected and stored for up to 3 days at 4°C. Embryos were cross-linked with 3% formaldehyde, extracts were prepared as described, and snap-frozen in liquid nitrogen for storage at -80°C. 20 grams of embryos were used for each experiment. S2 cell lines stably expressing BioTAP-N-Br140, BioTAP-N-dBRD4, and dBRD4-C-BioTAP were grown at 26.5°C to a density of ∼1 × 107 cells per milliliter using 500 mL of HyClone CCM3 serum-free medium in 2.8-L Fernbach glass flasks with shaking at 90 rpm. Cross-linked nuclear extracts from S2 cells were prepared from a total of 5 × 109 cells. After sonication, tandem affinity purification was performed to purify the BioTAP-tagged bait along with its protein interaction partners and associated genomic DNA. Genomic localization was determined by high-throughput sequencing of libraries generated from the tandem affinity-purified material using the NEBNext ChIP-seq library preparation master mix set for Illumina (New England Biolabs, catalog no. E6240S) and TruSeq adaptors (Illumina). Imaginal disc ChIP-seq was performed as described in Langlais et al (Langlais et al. 2012) with some modifications. 50~100 wing discs or haltere and 3rd leg discs were collected from dissection of 3rd instar larvae, crosslinked in 2% formaldehyde and sonicated using a BioRuptor (Diagenode) for 15 cycles (30 sec on/30 sec off) on high power. 5% of the total volume of sonicated chromatin was saved for input. ChIP was performed with 1:200 dilutions of anti-H3K27me3 (Cell Signaling), anti-H3K27ac (Active Motif). DNA was purified from immunoprecipitated samples. Illumina ChIP-seq libraries for H3K27me3 and H3K27ac were prepared using the library preparation kit (New England Biolabs) and sequenced as described above. Libraries for sequencing were prepared using standard Illumina protocols.

Platform Information


instrument_model
Illumina HiSeq 2000

External Database Query

Logs in read processing pipeline


Number of total reads
15653947
Reads aligned (%)
96.7
Duplicates removed (%)
8.9
Number of peaks
1527 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA