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| Status |
Public on Oct 18, 2016 |
| Title |
U2OS_exp1_vector_-Dox_rep2 |
| Sample type |
SRA |
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| Source name |
U2OS cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
treatment1(constitutive ha-omomyc or empty vector): vector
treatment2 (doxycycline to induce myc expression): Ethanol
antibody: non
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
U2OS_RNAseq_logFC.txt
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| 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.
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| Submission date |
Jan 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Eilers |
| Organization name |
University of Wuerzburg
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| Department |
Chair for Biochemistry and Molecular Biology
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| Lab |
Martin Eilers
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| Street address |
Am Hubland
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| City |
Wuerzburg |
| ZIP/Postal code |
97074 |
| Country |
Germany |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE77328 |
OmoMYC blunts promoter invasion by oncogenic MYC to inhibit gene expression characteristic of MYC-dependent tumors |
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| Relations |
| BioSample |
SAMN04445843 |
| SRA |
SRX1550254 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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