GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2589140 Query DataSets for GSM2589140
Status Public on Dec 20, 2017
Title SHEP_NMYCER_minusOHT_rep1
Sample type SRA
Source name SH-EP-NMYCER
Organism Homo sapiens
Characteristics treatment 1: EtOH
Treatment protocol For siRNA transfections, cells were transfected using the RNAiMAX reagent and OptiMem medium (LifeTechnologies) according to the manufacturer's instructions. Cells were harvested 48 h after transfection. Cells were treated with CD532 (1µM) or DMSO for 4 (ChIP-seq) or 4 and 8 (RNA-seq) hours.To activate N-MYC-ER in SH-EP cells, cells were treated with 4-OHT (200nM) for 5 hours. Conditional shRNA-mediated depletion of TFIIIC5 was induced with doxycycline (1 µg/ml) for 48 hours.
Growth protocol Neuroblastoma cells were grown in RPMI-1640 (Sigma). Medium was supplemented with 10% fetal calf serum (Biochrom) and penicillin/streptomycin (Sigma).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNeasy mini columns (Qiagen) including on-column DNase I digestion.
mRNA was extracted using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB). Library preparation was performed with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the instruction manual. Size-selection of libraries was performed using Agencourt AMPure XP Beads (Beckman Coulter) followed by amplification with 12 PCR cycles. Afterwards libraries were quantified and the size was determinded using Experion Automated Electrophoresis System (Bio-Rad).
For RNA-seq, reads were mapped to hg19 with Tophat2 and Bowtie1 with default settings.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description SHEP_NMYCER_plusOHT_vs_minusOHT.txt
Data processing Reads per gene were counted using the countOverlaps function from the R package {GenomicRanges}.
Weakly expressed genes were removed(mean count over all samples <1.5) and differentially expressed genes were called using EdgeR.
genome build: hg19
txt files containing Ensembl gene ID, gene symbol, gene description, log2FC, p-value and q-value (FDR) for all comparisons. A matrix file containing raw read counts for all samples.
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
Submission date Apr 25, 2017
Last update date May 15, 2019
Contact name Martin Eilers
Organization name University of Wuerzburg
Department Chair for Biochemistry and Molecular Biology
Lab Martin Eilers
Street address Am Hubland
City Wuerzburg
ZIP/Postal code 97074
Country Germany
Platform ID GPL18573
Series (1)
GSE78957 Association with Aurora-A controls N-MYC-dependent promoter escape and pause release of RNA polymerase II during the cell cycle
BioSample SAMN06831043
SRA SRX2764651

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap