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Sample GSM1231609 Query DataSets for GSM1231609
Status Public on Jul 10, 2014
Title U2OS_+Dox_RNAseq
Sample type SRA
 
Source name U2OS cells, +Dox, RNA
Organism Homo sapiens
Characteristics cell line: U2OS
doxycycline induction: +
Treatment protocol U2OS cells were induced with doxycycline (1µg/ml) for 30h.
Growth protocol U2OS cells were grown in DMEM (Sigma) supplemented with 10% fetal calf serum (PAA) and penicillin/streptomycin (PAA).
Extracted molecule total RNA
Extraction protocol For RNA-seq in U2OS cells, poly-A RNA was isolated from total RNA with Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific).
Library preparation was performed by using the NEBnext® mRNA Library Prep Master Mix set for Illumina (E6100S/L) following the instruction manual. Briefly, poly-A RNA was fragmented to generate 200 nucleotides fragments. First and second strand synthesis were performed and the resulting cDNA was end-repaired, ligated to NEBnext Adaptor, size selected (250bps) and purified with Qiagen gel extraction kit. cDNA was then amplified with 15 cycle of PCR and the resulting library was subjected to Illumina Genome Analyzer IIx sequencing according to the manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description This Sample represents 3 replicates.
Data processing Basecalling was performed with the RTA package within the Genome Analyzer Data Collection Software (SCS2.8).
Fastq files were generated by CASAVA only considering high quality sequences (PF-cluster).
Overall sequencing quality was checked with the FastQC script.
Reads were aligned to the human genome with BOWTIE v0.12.7 or v0.12.8 using default parameters.
Peak calling was performed with MACS v1.4.2 with default parameters, but: model fold 25 (HeLa-Myc) and 15 (HeLa-Miz1), duplicates 3 (U2OS-Myc) or 10 (U2OS-Miz1).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: .txt file from RNA-seq experiments contain ensembl-ID, gene symbol, log2 fold change, and p(adjust).
 
Submission date Sep 13, 2013
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 GPL10999
Series (1)
GSE44672 Activation and repression by oncogenic Myc shapes tumour-specific gene expression profiles
Relations
BioSample SAMN02356456
SRA SRX351412

Supplementary file Size Download File type/resource
GSM1231609_U2OS_+_-Dox_RNAseq.txt.gz 614.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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