Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SFPQ

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF-7, untreated, PSF ChIP
cell line
MCF-7
cell type
mammary adenocarcinoma cell line
treatment
none
capture oligo
N/A
antibody
anti-PSF

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, 10^8 MCF-7 cells (ATCC HTB-22) were crosslinked for 10 minutes with 1% formaldehyde. After nuclei isolation and sonication, sheared chromatin was incubated overnight with protein A beads bound to PSF antisera (clone 39-1; Santa Cruz Biotechnology, sc-101137, Lot # L1012). After incubation, beads were extensively washed and bound DNA was eluted through incubation with proteinase K at 55 degrees C for 1 hour. Eluted DNA was subjected to crosslink reversal overnight at 65 degrees C. DNA was purified using ethanol precipitation and subjected to library construction. Genomic DNA isolated by ChIP enrichment, as well as input DNA, was fragmented using sonication. Sonicated DNA was then subjected to end-repair, A-tailing, ligation to universal adapters, amplification with indexed primers, and size selection using SPRI beads.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
106322712
Reads aligned (%)
182.7
Duplicates removed (%)
1.5
Number of peaks
238661 (qval < 1E-05)

hg38

Number of total reads
106322712
Reads aligned (%)
184.8
Duplicates removed (%)
1.1
Number of peaks
228439 (qval < 1E-05)

Base call quality data from DBCLS SRA