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Sample GSM1233300 Query DataSets for GSM1233300
Status Public on Sep 17, 2016
Title DSN_NB4Atra24hrnaseq
Sample type SRA
 
Source name ATRA treated NB4 cells, 24h RNA
Organism Homo sapiens
Characteristics cell type: NB4 promyelocytic leukaemia cell line
treatment: ATRA 24h
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 total RNA
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 RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description RNA-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 GPL10999
Series (1)
GSE50958 Genome-wide epigenetic analyses and Transcriptional analysis in NB4 cells expressing PML-RARalpha
Relations
BioSample SAMN02358329
SRA SRX352352

Supplementary file Size Download File type/resource
GSM1233300_70H1GAAXX_2_2341_customTrack.bed.gz 52.8 Mb (ftp)(http) BED
GSM1233300_70H1GAAXX_2_2341_customTrack.wig.gz 8.3 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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