Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SLBP

Cell type

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

Attributes by original data submitter

Sample

source_name
HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr R749H
growth conditions
DMEM 10% FCS,+hygromycin+blasticidin+doxycycline+a-amanitin
antibody
rabbit anti SLBP (gift of Z. Dominski)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
cross-linked Chromatin was sonicated with a Bioruptor targeted ShapeMap on nascent RNA: IP's were prepared from DNAseI solublilized nuclear extracts (~1.5X 10E7 cells). Precipitated RNA was treated with 1M7 or DMS. RNA was purified by Trizol extraction. Prufied RNA was random primed and cDNA was PCR enriched for the 3' region of RD hisone transcripts and the 5' region of 18S rRNA. PCR fragments were converted to sequencing libraries using ChIP-seq library construction protocol. ChIP-seq: 1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
20279000
Reads aligned (%)
41.8
Duplicates removed (%)
21.5
Number of peaks
620 (qval < 1E-05)

hg38

Number of total reads
20279000
Reads aligned (%)
42.5
Duplicates removed (%)
20.7
Number of peaks
592 (qval < 1E-05)

Base call quality data from DBCLS SRA