Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Cdk12

Cell type

Cell type Class
Larvae
Cell type
3rd instar
NA
NA

Attributes by original data submitter

Sample

source_name
third instar larvae
tissue
whole tissue
genotype
wild type
chip antibody
CDK12 polyclonal (rabbit)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Using a ceramic mortar and pestle chilled with liquid N2, frozen larvae were ground to a powder and transferred to a homogenizer in ice-cold PBS. At room temperature, the homogenized cell suspensions were cross-linked with 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min and filtered through Miracloth. Chromatin pellets were collected and resuspended in ice-cold RIPA buffer, followed by sonicating in a Branson Digital Sonifer with 25% output for 10 min (2s on, 4 s off). For immunoprecipitation, Protein A Sepharose™ Fast Flow (GE Healthcare 17-5280-01) was pre-blocked, 4μl CDK12 polyclonal antibody were used for each immunoprecipitation. The input DNA and the IP DNA were purified with a PCR purification Kit (Qiagen28104) and eluted in TE buffer. DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads according to the DNA amount after each step. Library DNA was amplified by Phusion HF (NEB, Cat. M0530L). 2% agarose gel was used to select 200-500bp DNA fragments after PCR amplification.

Sequencing Platform

instrument_model
Illumina HiSeq 1500

dm3

Number of total reads
18880153
Reads aligned (%)
59.3
Duplicates removed (%)
36.7
Number of peaks
1758 (qval < 1E-05)

dm6

Number of total reads
18880153
Reads aligned (%)
55.6
Duplicates removed (%)
40.2
Number of peaks
2122 (qval < 1E-05)

Base call quality data from DBCLS SRA