Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CDK12

Cell type

Cell type Class
Bone
Cell type
143B
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
143B
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
39557475
Reads aligned (%)
62.3
Duplicates removed (%)
4.4
Number of peaks
1504 (qval < 1E-05)

hg38

Number of total reads
39557475
Reads aligned (%)
62.8
Duplicates removed (%)
3.3
Number of peaks
1538 (qval < 1E-05)

Base call quality data from DBCLS SRA