GSM5964391: 13-SW620-p53-rep1; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
TP53
Cell type
Cell type Class
Digestive tract
Cell type
SW 620
Primary Tissue
unresolved
Tissue Diagnosis
unresolved
Attributes by original data submitter
Sample
source_name
cell line
cell line
SW620
sequencing pool
ChIP Pool2
antibody
p53 IP
Sequenced DNA Library
library_name
GSM5964391
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA was isolated using Trizol reagent (ThermoFisher) or the AllPrep DNA/RNA/protein mini kit (Qiagen #80004) according to manufacturer recommendations. For ChIP-seq, HCT116, HCT8, DLD1, and SW620 cells were cross-linked with formaldehyde (1% final) for 10 min at room temperature. Cross-linked cells were quenched with glycine (125 mM final) for 5 min, followed by two washes in cold PBS. Nuclei were then isolated from 20 million cells as previously described (67), and chromatin was sheared to 250-bp average size using a Covaris S220. Immunoprecipitations were performed using 1000 μg of sheared chromatin lysate and 5 μg of p53 antibody (p53 D07; Santa Cruz, sc-47698) preconjugated to protein G beads (Invitrogen). ChIP reactions were incubated for 16 hours at 4°C with rotation and then washed four times in wash buffer [50 mM Hepes-HCl (pH 8), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, and 0.5% N-laurylsarcosine], followed by one wash in ChIP final wash buffer (1× tris-EDTA (TE) Buffer and 50 mM NaCl). Immunoprecipitated DNA was eluted from washed beads, reverse cross-linked overnight, purified, and used to construct libraries. Clontech/Takara SMARTer Stranded Total RNA-seq PICO v2 kit (Clontech/Takara 634414) for RNA-seq. For ChIP-seq, libraries were prepared using NEBNext Ultra reagents (New England Biolabs).