Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CDK12

Cell type

Cell type Class
Bone
Cell type
MG-63
Primary Tissue
Bone
Tissue Diagnosis
Osteosarcoma

Attributes by original data submitter

Sample

source_name
highly metastatic osteosarcoma cell line
tissue
highly metastatic osteosarcoma cell line
cell line
MG63-3
chip antibody
anti-CDK12 (gift from Arno Greenleaf)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-Seq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For RNA-Seq samples, cells were lysed and RNA extracted with TRIzol according to the manufacturer's protocol. ChIP-Seq libraries were prepared as previously described (Schmidt et al. 2009). For RNA-seq, Total RNA was treated with DNase I (Invitrogen, Carlsbad, CA). RNA was spiked-in with ERCC RNA Spike-In Mix (Ambion, Foster City, CA) and analyzed on an Agilent Bioanalyzer 2100 for integrity. PolyA+ RNA was isolated using the Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer's protocol. For Whole Genome Sequencing, PCR-free libraries were prepared from MG63.3-GFP and 143B-GFP cells using TruSeq DNA PCR-Free High Throughput Library Prep Kit (Illumina, 20015963) and following the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
91862202
Reads aligned (%)
71.6
Duplicates removed (%)
6.3
Number of peaks
1140 (qval < 1E-05)

hg38

Number of total reads
91862202
Reads aligned (%)
72.2
Duplicates removed (%)
5.4
Number of peaks
1314 (qval < 1E-05)

Base call quality data from DBCLS SRA