Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Pc

Cell type

Cell type Class
Cell line
Cell type
ML-DmBG3-c2
Source
y[1] v[1] f[1] mal[F1]
Tissue Source
central nervous system
Developmental Stage
third instar larval stage

Attributes by original data submitter

Sample

source_name
BG3C2 cells
antibody
Pc, Santa Cruz #sc-25762
genotype/variation
DMAD-siRNA knockdown

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Genomic DNA was prepared following regular protocol as described previously4 with some modifications. Add 600 μl of lysis buffer containing 100mM Tris-HCl, pH 8.5, 5mM EDTA pH8.0, 0.2% SDS, 200mM NaCl, and 20-25 μl of protease K @ 20mg/ml to the ground tissues or cells, mix well, and incubate at 55°C overnight. After the overnight digestion was cooled down to room temperature, add 5 μl of RNase A solution @ 20mg/ml for at least 1hr at RT. Following extraction with equal volume of phenol: chloroform: isoamyl alchohal =25:24:1, precipitation was carried out using equal volume of isopropanol. If flocky DNA forms, transfer it to a new tube containing 1ml of 70% ethanol. If necessary, spin down to collect the remained DNA in the precipitation solution followed by washing with 70% ethanol. If no flocky DNA appears, spin down @maximum speed for 10 min to collect gDNA pellet. 25ng of input genomic DNA or experimental enriched DNA were utilized for each library construction. 150-300 bp DNA fragments were selected by AMPure XP Beads (Beckman Coulter) after the adapter ligation. An Agilent 2100 BioAnalyzer was used to quantify the amplified DNA, qPCR was applied to accurately quantify the library concentration. 20 pM diluted libraries were used for sequencing. 50-cycle single-end sequencings were performed using Illumina HISeq 2000. Image processing and sequence extraction were done using the standard Illumina Pipeline. RNA-seq libraries were generated from duplicated samples per condition using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer’s protocol. The RNA-seq libraries were sequenced as 50-cycle pair-end runs using Illumina HiSeq 2000.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

dm3

Number of total reads
8573437
Reads aligned (%)
73.0
Duplicates removed (%)
23.8
Number of peaks
2573 (qval < 1E-05)

dm6

Number of total reads
8573437
Reads aligned (%)
70.3
Duplicates removed (%)
25.8
Number of peaks
2732 (qval < 1E-05)

Base call quality data from DBCLS SRA