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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.
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|
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer IIx |
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|
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).
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|
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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 |