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Sample GSM2050635 Query DataSets for GSM2050635
Status Public on Jul 11, 2016
Title RNAseq_titration_Dox0.05_rep2
Sample type SRA
 
Source name U2OS cells
Organism Homo sapiens
Characteristics antibody: non
cell line: U2OS
Treatment protocol Cells were grown with the indicated doxycycline concentration for 30h.
Cells were grown with the indicated doxycycline concentration for 30h.
Growth protocol U2OS cells were grown in DMEM (Sigma) suppelmented with 10% FCS (Biochrom) and penicillin/streptomycin (Sigma).
U2OS cells were grown in DMEM (Sigma) suppelmented with 10% FCS (Biochrom) and penicillin/streptomycin (Sigma).
Extracted molecule total RNA
Extraction protocol For RNA-seq, total RNA was extracted using the RNeasy mini columns (Qiagen) including on-column DNase I digestion.
PolyA+-RNA was isolated from total with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB). The NEBNext® Ultra™ RNA Library Prep Kit for Illumina was used for library preparation following the manufacturer’s instruction. Size selection of the libraries was performed with the AMPure XP Beads (Beckman Coulter), followed by 12 PCR cycle for amplification. Library quantification and quality was assessed using the Experion Automated Electrophoresis System (Bio-Rad).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description RNAseq_titration_logFC.txt
Data processing RNA-seq:
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 o the human genome using Bowtie v0.12.8. with default parameters.
Bam files were generated using Samtools v0.1.18.
Raw count tables for each ensembl gene were generated using the summarizeOverlaps {GenomicAlignments} function in R.
Differentially expressed genes were called using the edgeR package in R.
hg19
txt file containing log2FC, p-value and adjusted p-value. For detailed description see additional README.txt. Raw count matrices are provided as txt file.
Supplementary_files_format_and_content: fixedStep wiggle files
 
Submission date Jan 28, 2016
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)
GSE77356 Different promoter affinities account for specificity in MYC-dependent gene regulation
Relations
BioSample SAMN04447448
SRA SRX1552468

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

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