Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMC1A

Cell type

Cell type Class
Lung
Cell type
A549
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
A549-CHIP-SMC1A
cell line
A549 (ATCC, CCL-185)
cell type
Lung adenocarcinoma-derived cells
passages
9
treated with
0.01% EtOH, 60min
chip antibody
SMC1 (Bethyl, A300-055A, lot:3)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde in culture medium for 10 minutes at room temperature. Cells were then lysed in 10 ml lysis buffer (0.1%SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl ph 8.0 and 150 mM NaCl) and chromatin was sheared to 200-600 bp fragments using a Bioruptor Sonicator (Diagenode). Chromatin extract from 5x10^7 cells was incubated overnight at 4oC with 100 ul of Dynabeads Protein G magnetic beads (Life Technologies, 10004D) previously incubated with 10 ug of selected antibodies. After ChIP, samples were washed and bound complex were reversed cross-linked and eluted in 10mM Tris-HCl pH 8 The TruSeq DNA sample prep kit with indexing adapters was used according to the manufacturer's recommendations (Illumina)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
40562175
Reads aligned (%)
89.2
Duplicates removed (%)
4.1
Number of peaks
39493 (qval < 1E-05)

hg38

Number of total reads
40562175
Reads aligned (%)
90.5
Duplicates removed (%)
3.4
Number of peaks
39635 (qval < 1E-05)

Base call quality data from DBCLS SRA