|
| Status |
Public on Mar 26, 2019 |
| Title |
siCTRL replicate 1 IL-1 |
| Sample type |
SRA |
| |
|
| Source name |
bone
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: U2OS osteosarcoma, epithelial
treatment: 1h IL-1 beta (2ng/ml final)
genotype: siMM, control
|
| Treatment protocol |
Cells were transcfected with either a mis-match Control (siCTRL) or ZNF598-specific (siZNF598) siRNAs using RNAiMAX (Life Technologies) and were left non-stimulated (ns) or stimulated with IL-1 beta (2ng/ml final concentration, Peprotech) for 1h
|
| Growth protocol |
U2OS cells were maintained and propagated in DMEM medium supplemented with 10% fetal calf serum and Pen/Strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After stimulation cells were directly lyzed in TRIZol and total RNAs were extracted according to the manufacturer's protocol
Total RNA libraries were generated using the NEBNext Ultra II Directional RNA Library Kit (New England Biolabs #E7765) after rRNA-depletion using the NEBNext rRNA depletion kit (New England Biolabs #6310). To facilitate multiplexing oif libraries indexed primers (New England Biolabs #E7335) were used. 500 ng of total RNA per sample were used as input material.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
NEBNext index 3 primer
|
| Data processing |
All steps except demultiplexing were performed in the Galaxy suite.
After demultiplexing fastq files were groomed (FASTQ Groomer Galaxy Version 1.0.4) and adapter- and quality-trimmed using "Trim Galore!" (Galaxy Version 0.4.2). The reads were then mapped against hg19 (b37) using RNA STAR (Galaxy Version 2.5.2b-0)
For differential gene expression analysis, count tables from the mapped sequencing data were generated and used in DeSeq2 to identify regulated transcripts.
Genome_build: hg19 (b37)
Supplementary_files_format_and_content: The different DeSeq2 comparisons are provided as tab-delimited .txt files
|
| |
|
| Submission date |
Jun 21, 2018 |
| Last update date |
Mar 26, 2019 |
| Contact name |
Christopher Tiedje |
| E-mail(s) |
tiedje@sund.ku.dk
|
| Organization name |
University of Copenhagen
|
| Department |
Department of Molecular and Cellular Medicine (ICMM)
|
| Lab |
Simon Bekker-Jensen
|
| Street address |
Blegdamsvej 3B
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE116126 |
A role for ZNF598 in post-transcriptional gene regulation |
|
| Relations |
| BioSample |
SAMN09466845 |
| SRA |
SRX4278343 |
