Illumina HiSeq 2000 sequencing; ChIP-seq for H2Bub1, H3K27ac and H3K79me3 in SW837 cells
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
Input control
Antigen
Input control
Cell type
Cell type Class
Digestive tract
Cell type
SW 837
Primary Tissue
Rectum
Tissue Diagnosis
Adenocarcinoma
Attributes by original data submitter
Sample
Alias
E-MTAB-7786:SW837 Input 2
Broker name
ArrayExpress
Description
Protocols: SW837 cells were grown in DMEM/F-12 medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin and 100 μg/ml streptomycin at 37°C and 5% CO2. Upon washing with PBS, cells were crosslinked with 1% formaldehyde for 20 minutes and quenched using 125 mM glycine. Upon scraping, nuclear pellets were prepared in and washed with the nuclear preparation buffer (150mM NaCl, 20 mM EDTA, 50 mM Tris-HCl (pH 7.5), 0.5% v/v NP-40, 1% v/v Triton-X-100, 20 mM NaF). Samples were sonicated in sonication buffer (150mM NaCl, 20 mM EDTA, 50 mM Tris-HCl (pH 8), 1% v/v NP-40, 0.5% v/v Sodium deoxycholate, 20 mM NaF, 0.1% SDS) for 20 cycles (30s on/off). Samples were precleared using 50% Sepharose 4B slurry (GE Healthcare) and incubated with the respective antibodies overnight: H3K27ac (196-050, Diagenode), H3K79me3 (C15310068, Diagenode) and H2Bub1 (55465, Cell Signaling). Sepharose beads with Protein A (for rabbit antibodies) or Protein G (for mouse antibodies) were added to samples and incubated for 2 hours followed by washes, de-crosslinking, and DNA extraction. DNA extraction was performed using Roti(R)-phenol/chloroform/Isoamylalcohol (Roth) followed by precipitation in 100% ethanol and washes with 70% ethanol. Libraries for DNA from ChIP were made using the NEBNext Ultra DNA library preparation kit according to the manufacturer’s instructions.
ENA checklist
ERC000011
INSDC center alias
University Medical Center Gottingen Clinic for General, Visceral and Pediatric Surgery Tumor Epigenetics
INSDC center name
University Medical Center Gottingen Clinic for General, Visceral and Pediatric Surgery Tumor Epigenetics
INSDC first public
2019-07-08T17:04:29Z
INSDC last update
2019-03-15T16:43:15Z
INSDC status
public
SRA accession
ERS3230406
Sample Name
ERS3230406
Title
SW837 Input 2
cell_line
SW837
disease
rectal adenocarcinoma
organism
Homo sapiens
organism part
rectum
replicate
2
Sequenced DNA Library
library_name
SW837 Input 2_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
SW837 cells were grown in DMEM/F-12 medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin and 100 μg/ml streptomycin at 37°C and 5% CO2. Upon washing with PBS, cells were crosslinked with 1% formaldehyde for 20 minutes and quenched using 125 mM glycine. Upon scraping, nuclear pellets were prepared in and washed with the nuclear preparation buffer (150mM NaCl, 20 mM EDTA, 50 mM Tris-HCl (pH 7.5), 0.5% v/v NP-40, 1% v/v Triton-X-100, 20 mM NaF). Samples were sonicated in sonication buffer (150mM NaCl, 20 mM EDTA, 50 mM Tris-HCl (pH 8), 1% v/v NP-40, 0.5% v/v Sodium deoxycholate, 20 mM NaF, 0.1% SDS) for 20 cycles (30s on/off). Samples were precleared using 50% Sepharose 4B slurry (GE Healthcare) and incubated with the respective antibodies overnight: H3K27ac (196-050, Diagenode), H3K79me3 (C15310068, Diagenode) and H2Bub1 (55465, Cell Signaling). Sepharose beads with Protein A (for rabbit antibodies) or Protein G (for mouse antibodies) were added to samples and incubated for 2 hours followed by washes, de-crosslinking, and DNA extraction. DNA extraction was performed using Roti(R)-phenol/chloroform/Isoamylalcohol (Roth) followed by precipitation in 100% ethanol and washes with 70% ethanol. Libraries for DNA from ChIP were made using the NEBNext Ultra DNA library preparation kit according to the manufacturer's instructions.