Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Dll

Cell type

Cell type Class
Larvae
Cell type
Imaginal leg disc
NA
NA

Attributes by original data submitter

Sample

source_name
Third instar leg imaginal discs
genotype
yw
developmental stage
L3
tissue
leg imaginal disc
antibody
ChIP with anti-Dll

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Third instar larvae were dissected in PBS and fixed for 20 minutes at room temperature in 1.8% formaldehyde, 50mM HEPES, 1mM EDTA, 0.5mM EGTA, 100mM NaCl. After quenching (0.125M Glycine, 1xPBS, 0.01% Triton) the fixed tissue was washed first in Buffer A (10mM HEPES, 10mM EDTA, 0.5mM EGTA, 0.25% Triton, 1mM PMSF), then in Buffer B (10mM HEPES, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.01% Triton, 1mM PMSF), for 10 minutes at 4C. Imaginal discs were then dissected off the cuticles in Buffer B. Discs were sonicated in Buffer C (10mM HEPES, 1mM EDTA, 0.5mM EGTA, 1mM PMSF, plus complete protease inhibitor cocktail (Roche)) on ice/EtOH. Soluble chromatin was transferred to new tubes after centrifugation. Fresh chromatin, precleared with protein G sepharose beads (Roche), was incubated overnight at 4C with antibody in RIPA buffer (140mM NaCl, 10mM HEPES, 1mM EDTA, 1% Glycerol, 1% Triton X-100, 0.1% DOC, 1mM PMSF). Antibody-chromatin complexes were pulled down with protein G sepharose beads for 3 hours at 4C. Bound beads were washed 4-times in RIPA buffer (as above plus 0.1mg/mL ssDNA) and once in TE. Chromatin was eluted twice in Elution Buffer (1% SDS, 0.1M NaHCO3). 20ug Proteinase K was added, and samples were incubated for 3 hours at 55C, then 65C overnight. DNA was purified via phenol-chloroform extraction and ethanol precipitation. DNA samples were prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Preparation Kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

dm3

Number of total reads
19091508
Reads aligned (%)
74.5
Duplicates removed (%)
22.2
Number of peaks
0 (qval < 1E-05)

dm6

Number of total reads
19091508
Reads aligned (%)
72.1
Duplicates removed (%)
24.5
Number of peaks
1369 (qval < 1E-05)

Base call quality data from DBCLS SRA