Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Su(var)205

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
CDK12 knockdown
chip antibody
HP1a 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 HP1a polyclonal antibody or 3μl H3K9me2 antibody (Ab1220) 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. Libraries were constructed according to Hiseq 2500 rapid SR50 one flowcell sequencing instructions

Sequencing Platform

instrument_model
Illumina HiSeq 2500

dm3

Number of total reads
44147907
Reads aligned (%)
97.7
Duplicates removed (%)
24.8
Number of peaks
8299 (qval < 1E-05)

dm6

Number of total reads
44147907
Reads aligned (%)
96.0
Duplicates removed (%)
32.5
Number of peaks
0 (qval < 1E-05)

Base call quality data from DBCLS SRA