Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CDK11A

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
HCT116
tissue
HCT116 cells
method
ChIP-seq CDK11
condition
CDK11_ChIP_G2_M_phase_8h
strain
HCT116 Flp-in
antibody
Abcam CDK11 (ab19393)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed with Abcam CDK11 antibody (ab19393). Protein G Dynabeads (Thermo Fisher Scientific, 10009D) were pre-blocked with BSA for 4 h, washed 3 times with RIPA buffer (50 mM Tris-Cl, pH 8, 150 mM NaCl, 5 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, supplemented with protease inhibitors, Sigma, P8340), followed by the incubation with specific antibody for at least 4 h at 4°C. Cells were crosslinked with 1% formaldehyde for 10 min, reaction was quenched with glycine (final concentration 125 mM) for 5 min. Cells were washed twice with ice-cold PBS, scraped, and pelleted. Each 20 µl packed cell pellet was lysed in 650 µl of RIPA buffer and sonicated 20 x 7s (amp 0.85) using 5/64 probe (QSonica Q55A). Clarified extracts (13,000g for 10 min) were precleared with protein G Dynabeads rotating for 2-4 h at 4°C and then incubated overnight with antibody pre-bound to protein G Dynabeads. For each ChIP-seq experiment (CDK11) we performed 3 technical replicates, dissolved each replicate in 17 µl of water and pooled them together to get at least 2.5 ng of immunoprecipitated DNA before library preparation (measured by Qubit). ChIP-seq libraries were generated using the KAPA Biosystems Hyper Prep Kit (KK8502) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and Set 2 (NEB E7335S, E7500S). Libraries were sequenced (50-bp single-end reads) using an Illumina HiSeq 2500 (VBCF Vienna).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
20503887
Reads aligned (%)
89.4
Duplicates removed (%)
9.0
Number of peaks
795 (qval < 1E-05)

hg38

Number of total reads
20503887
Reads aligned (%)
91.1
Duplicates removed (%)
8.0
Number of peaks
578 (qval < 1E-05)

Base call quality data from DBCLS SRA