Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
yki

Cell type

Cell type Class
Cell line
Cell type
S2
Source
Oregon R
Developmental Stage
late embryonic stage

Attributes by original data submitter

Sample

source_name
S2 cell line ChIP; Yki antibody
developmental stage
S2 (embryo cell line)
cell line
S2
chip antibody
anti-Yki

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin lysates were clarified from homogenized and sonicated tissues; protein-DNA complexes were isolated with antibody. DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911). Briefly, up to 12.5 ng DNA was included in the high molecular weight (HMW) tagmentation reaction (5 minutes at 55 degrees Celsius). Tagmented DNA was purified using a Qiagen MinElute column. Addition of barcoded PCR-compatible sites and library enrichment were performed using 12 cycles of PCR. Amplified DNA was purified using the Qiagen MinElute PCR Purification Kit. Library fragments of approximately 225 bp were gel purified and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on a HiSeq2000 according to the manufacturer’s protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

dm3

Number of total reads
25264926
Reads aligned (%)
70.3
Duplicates removed (%)
23.5
Number of peaks
0 (qval < 1E-05)

dm6

Number of total reads
25264926
Reads aligned (%)
67.9
Duplicates removed (%)
25.8
Number of peaks
0 (qval < 1E-05)

Base call quality data from DBCLS SRA