Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ASXL3

Cell type

Cell type Class
Lung
Cell type
NCI-H1963
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma Small Cell

Attributes by original data submitter

Sample

source_name
ASXL3_Ab1_H1963
cell line
NCI-H1963
tissue
small cell lung cancer
passages
Low passages (6-10)
antibody
anti-ASXL3-1 (homemade)
treatment
Parental cells

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit. RNA-seq: Paramagnetic beads coupled with oligo d(T) are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual. Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer's recommendation (NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®). The first strand is synthesized with the Protoscript II Reverse Transcriptase with an longer extension period (40 minutes for 42◦C). All remaining steps for library construction were used according to the NEBNext® Ultra™ II RNA Nondirectional Library Prep Kit for Illumina®. Illumina 8-nt dual-indices were used. Samples were pooled and sequencing on a HiSeq with a read length configuration of 150 PE. ChIP-seq: ChIP-sequencing libraries were prepared using KAPA HyperPrep Kit (Kapa Biosystems) following manufacturer's recommendation. In brief, 500ng of input DNA sheared by Covaris LE220 ultrasonicator or 10 ng of immunoprecipitated DNA was end-repaired and 3'-dA tailed. Adapter was then ligated to the DNA, and ligated product was PCR amplified and cleaned up using SPRIselect Reagent (Beckman Coulter).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
17307356
Reads aligned (%)
78.9
Duplicates removed (%)
8.7
Number of peaks
5012 (qval < 1E-05)

hg38

Number of total reads
17307356
Reads aligned (%)
79.6
Duplicates removed (%)
8.5
Number of peaks
5083 (qval < 1E-05)

Base call quality data from DBCLS SRA