|
| Status |
Public on Sep 17, 2016 |
| Title |
NB4_MC2392_4h_ChIP_Seq |
| Sample type |
SRA |
| |
|
| Source name |
MC2392 treated NB4 cells, 4h ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: NB4 promyelocytic leukaemia cell line
treatment: MC2392 4h
chip antibody: H3K9K14ac (Diagenode)
reference genome: HG18
|
| Treatment protocol |
NB4 cells were treated with ATRA, MS275 and MC2392
|
| Growth protocol |
NB4 cells were grown at 37°C in air and 5% CO2 in RPMI 1640 medium (EUROCLONE),supplemented with 10% heat-inactivated fetal bovine serum (FBS, Sigma), ampicillin/streptomycin and 0.1% gentamicin (SIGMA).1% L-glutamine, 1%
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was sonicated and used for ChIP-seq using H3K9K14ac (Diagenode). RNA was extracted using qiagen RNeasy kit according to manufacturer. cDNA first and Ds-cDNA synthesis then, was performed following supplier’s instructions (Invitrogen). Ds-cDNA samples were prepared for sequencing by end repair of 20 ng DNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (~300 bp) and limited PCR amplification (14 cycles). The resulting sample libraries were subjected to DSN treatment (Evrogen) according to the manufacturer’s recommendations.
ChIP and RNA seq libraries were preapared according to Illumina's standard protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
chromatin IP (ChIP-seq)
|
| Data processing |
Basecalls performed using CASAVA
Reads were aligned to the hg18 genome assembly using ELAND
Peaks were called using MACS 1.3.3 on settings:mfold =32, tsize=32, p value = e-6
Genome_build: All ChIP-seq tracks were mapped to genome build HG18, RNA-seq tracks were mapped to HG18.
Supplementary_files_format_and_content: wig files were generated (extended to 300bps)
|
| |
|
| Submission date |
Sep 17, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
H.G. Stunnenberg |
| E-mail(s) |
h.stunnenberg@ncmls.ru.nl
|
| Phone |
+31-24-3610520
|
| Organization name |
Radboud University
|
| Department |
Department of Molecular Biology (274)
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE50958 |
Genome-wide epigenetic analyses and Transcriptional analysis in NB4 cells expressing PML-RARalpha |
|
| Relations |
| BioSample |
SAMN02358323 |
| SRA |
SRX352348 |
