Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ASXL1

Cell type

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

Attributes by original data submitter

Sample

source_name
Flp-In HEK293 T-REx cell line
cell line
Flp-In HEK293 T-REx
chip antibody
Anti-ASXL1 (sc85283), Santa Cruz Biotechnology

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin fixation and immunoprecipitation were performed essentially as described in Orlando et al. (1997; PMID:8993033). Cells (3-4x108) were fixed in 200 mL of medium with 1% formaldehyde for 10 min at room temperature. Cross-linked cells were sonicated to produce chromatin fragments of an average size of 150–400 bp. Soluble chromatin was separated from insoluble material by centrifugation. The supernatant containing chromatin of 1-2x107 cells was used for immunoprecipitation. Sequencing libraries were prepared with the NEB Genomic DNA Sample Preparation Kit according to NEB’s instructions. After adapter ligation, library fragments of 250-350 bp were isolated from an agarose gel. The DNA was PCR amplified with Illumina primers with 18 cycles, purified, and loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx (TrueSeq cBot-GA v2 and TruSeq v5 SBS kit) and HiSeq 2000 (HiSeq Flow Cell v3 and TruSeq SBS Kit v3) following the manufacturer’s protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
47202241
Reads aligned (%)
39.3
Duplicates removed (%)
56.1
Number of peaks
20578 (qval < 1E-05)

hg38

Number of total reads
47202241
Reads aligned (%)
40.6
Duplicates removed (%)
54.9
Number of peaks
20315 (qval < 1E-05)

Base call quality data from DBCLS SRA