Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Larvae
Cell type
CNS and imaginal discs
NA
NA

Attributes by original data submitter

Sample

source_name
3rd instar brains and imaginal disks, Pho input
strain/background
ry
developmental stage
3rd instar larvae
tissue
CNS and imaginal disks
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Fixed brains and imaginal discs were dissected from 10 third instar larvae. Sonicated chromatin incubated with anti ChIP was performed with 1:100 dilutions of anti-Pho (custom made) and anti-Ph antibodies (a kind gift from Donna Arndt-Jovin), 1:200 dilutions of anti-H3K27me3 (Millipore, 17-622) antibodies, and anti-Engrailed antibodies. Input ChIP DNA (30 ng) was blunt-ended and phosphorylated. A single 'A' nucleotide was added to the 3' ends of the fragments in preparation for ligation to an adapter that has a single-base 'T' overhang. The ligation products were purified and accurately size-selected by agarose gel electrophoresis. Size-selected DNA was purified and PCR-amplified to enrich for fragments that have adapters on both ends. The final purified product was then quantitated before cluster generation.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

dm3

Number of total reads
28924023
Reads aligned (%)
54.4
Duplicates removed (%)
25.6
Number of peaks
1935 (qval < 1E-05)

dm6

Number of total reads
28924023
Reads aligned (%)
53.4
Duplicates removed (%)
28.7
Number of peaks
2120 (qval < 1E-05)

Base call quality data from DBCLS SRA