Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
cnc

Cell type

Cell type Class
Adult
Cell type
Adult female
NA
NA

Attributes by original data submitter

Sample

source_name
AdultFemale
developmental stage
AdultFemale
fraction
ChIP
replicate
2
transcription factor
cnc
antibody name
KW0-cnc
antibody manufacturer
White Lab
antibody catalog number
KW0-cnc

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. Libraries were prepared according to ChIP-seq library kit instruction Nextera DNA prep kit is FC-121-103

Sequencing Platform

instrument_model
Illumina HiSeq 2000

dm3

Number of total reads
23287832
Reads aligned (%)
71.2
Duplicates removed (%)
19.6
Number of peaks
0 (qval < 1E-05)

dm6

Number of total reads
23287832
Reads aligned (%)
69.8
Duplicates removed (%)
21.0
Number of peaks
0 (qval < 1E-05)

Base call quality data from DBCLS SRA