Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GFP

Cell type

Cell type Class
Adult
Cell type
Adult
NA
NA

Attributes by original data submitter

Sample

source_name
Whole organism
strain
N2; Is[pvha-6::klf-1-yfp]
developmental stage
First day of adulthood
tissue
Whole body
antibody
GFP-TRAP (Chromotek; Cat. #gtma-20; Lot. 81025001MA)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were sonicated and cleared by centrifugation. Protein-DNA complexes were pulled-down using GFP-TRAP (Chromotek). Libraries were prepared by using the Illumina TruSeq DNA Nano Kit with some modifications. The preparation was started with the end repair step of the protocol. Up to 100ng ChIP/Input DNA was used as starting material. After end repair and A-tailing dual indexing adapters were ligated. The products were then purified and amplified (12 PCR cycles for the Input Samples and 15 cycles for the ChIP Samples) to create the final libraries. After validation (Agilent 4200 TapeStation) each single library was quantified by using the Roche KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System. The libraries were then pooled equimolar. Finally the pool was sequenced on one Illumina HiSeq4000 lane 1x51bp (51+8+8).

Sequencing Platform

instrument_model
Illumina HiSeq 4000

ce11

Number of total reads
27392700
Reads aligned (%)
72.2
Duplicates removed (%)
47.3
Number of peaks
825 (qval < 1E-05)

ce10

Number of total reads
27392700
Reads aligned (%)
72.2
Duplicates removed (%)
47.3
Number of peaks
823 (qval < 1E-05)

Base call quality data from DBCLS SRA