Curated Sample Data


Genome
dm3
Antigen Class
Input control
Antigen
Input control
Cell type Class
Larvae
Cell type
3rd instar

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
third instar larvae
tissue
whole tissue
genotype
wild type
chip antibody
none

Metadata from Sequence Read Archive

Library Description


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.

Platform Information


instrument_model
Illumina HiSeq 1500

External Database Query

Logs in read processing pipeline


Number of total reads
17724933
Reads aligned (%)
89.5
Duplicates removed (%)
12.5
Number of peaks
1613 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA