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Sample GSM2049346 Query DataSets for GSM2049346
Status Public on Oct 18, 2016
Title KPC_OmoMYC_-Dox_rep1
Sample type SRA
 
Source name KPC cells
Organism Mus musculus
Characteristics cell line: KPC
treatment1(constitutive ha-omomyc or empty vector): HA-OmoMYCwt
treatment2 (doxycycline to induce myc expression): Ethanol
antibody: non
Extracted molecule total RNA
Extraction protocol For RNA-sequencing, 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 cycles 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 NextSeq 500
 
Description KPC_RNAseq_logFC.txt
Data processing For RNA-seq, fastq files were mapped using Bowtie2 v2.2.4 (KPC cells, mm9) or TopHat v2.0.7 (U2OS cells, hg19).
Reads per gene were counted using the countOverlaps function from the R package {GenomicRanges}.
Weakly expressed genes were removed (U2OS: mean CPM over all samples <1) and differentially expressed genes were called using EdgeR.
hg19 for U2OS cells, mm9 for KPC cells
txt files containing Ensembl gene ID, gene symbol, gene description, log2FC, p-value and q-value for each comparison described in RNAseq_README.txt
Fastq files were generated using Illumina's CASAVA software.
 
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 GPL19057
Series (1)
GSE77328 OmoMYC blunts promoter invasion by oncogenic MYC to inhibit gene expression characteristic of MYC-dependent tumors
Relations
BioSample SAMN04445822
SRA SRX1550277

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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