|
| Status |
Public on Jul 11, 2016 |
| Title |
RNAseq_titration_Dox0.0_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 |
SAMN04447451 |
| SRA |
SRX1552471 |
