Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMN1

Cell type

Cell type Class
Kidney
Cell type
293
Primary Tissue
Kidney
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HEK293
cell type
HEK293
genotype/variation
Expressing Dox inducible GFP-SMN fusion protein. Construct is hygromycin resistant.
antibody
SMN (Santa Cruz pAb Cat # H-195)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
10e7-10e8 cells were cross-linked for 10 min in 1% formaldehyde. Lysates were sonicated to a DNA fragment length range of 200-300 bp using a Bioruptor (Diagenode). RNAPII was immunoprecipitated with 2ug of antibodies and Dynabeads Protein G (Invitrogen). Subsequently, crosslinks were reversed at 65°C over night and bound DNA fragments were purified (EZ-10 Spin Column PCR Product Purification kit, Bio Basic). Sequencing libraries were constructed using the TruSeq ChIP Sample Prep Kit (Illumina) according the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
42646096
Reads aligned (%)
89.1
Duplicates removed (%)
5.8
Number of peaks
1042 (qval < 1E-05)

hg38

Number of total reads
42646096
Reads aligned (%)
90.5
Duplicates removed (%)
4.9
Number of peaks
912 (qval < 1E-05)

Base call quality data from DBCLS SRA