Csp6I
1st restriction digest
DpnII
2nd restriction digest
2021-05-03
ENA first public
2020-12-15
ENA last update
ERC000011
ENA-CHECKLIST
SAMEA7722606
External Id
MPIMG
INSDC center alias
Max Planck Institute for Molecular Genetics
INSDC center name
2021-05-03T00:21:55Z
INSDC first public
2020-12-15T12:54:47Z
INSDC last update
public
INSDC status
ERS5469985
SRA accession
E-MTAB-9915:4C-seq_IntronicViewpoint_dex_dex_rep1
Submitter Id
ArrayExpress
http://www.ebi.ac.uk/efo/EFO_0009737
broker name
A549
http://www.ebi.ac.uk/efo/EFO_0001086
cell line
human
http://purl.obolibrary.org/obo/NCBITaxon_9606
common name
Protocols: 4C-seq was performed with 5 million cells per treatment, cells were grown in DMEM containing 5% fetal bovine serum. A549 cells were grown to approximately 90% confluence according to standard protocols in DMEM medium with 5% FBS. Cells were treated with either 100 nM dexamethasone or 0.1% ethanol. After 4 hours, cells were washed 2x with PBS and cultured in hormone-free medium for 24 hours, after which cells were treated again for 4 hours with either 100 nM dexamethasone or 0.1% ethanol. 4C template preparation was carried out as described in PMID: 22929766. Restriction digests were performed with the enzymes Csp6I (primary, Thermo Fisher Scientific) and DpnII (secondary, Thermo Fisher Scientific). 4C-seq library preparation was performed as described in PMID: 31351925 (except that the DNA was purified with 1.5× AMPure XP beads (Beckman Coulter) after the first PCR). The following primer pairs were used for the inverse PCR: ZBTB16 promoter-proximal VP (fwd: TACACGACGCTCTTCCGATCTAGCAGAGAGGAGTTGAGG, rev: ACTGGAGTTCAGACGTGTGCTCTTCCGATCTTAGTGAACCAGGTGCCAG), ZBTB16 intronic VP (fwd: TACACGACGCTCTTCCGATCTATGTGTGCGTTCATGTATGT, rev: ACTGGAGTTCAGACGTGTGCTCTTCCGATCTGAGGAAAGGTTAGGAAGTGG)
description
adult
developmental stage
carcinoma
http://www.ebi.ac.uk/efo/EFO_0000313
disease
Homo sapiens
http://purl.obolibrary.org/obo/NCBITaxon_9606
organism
Homo sapiens
http://purl.obolibrary.org/obo/NCBITaxon_9606
organism
lung
http://purl.obolibrary.org/obo/UBERON_0002048
organism part
4C-seq_IntronicViewpoint_dex_dex_rep1
title
chr11:114051224-114051804 (hg19)
viewpoint