|
| Status |
Public on Jan 01, 2019 |
| Title |
THP1 TRIPZ-shRUVBL2 DOX-2 DAY 2 |
| Sample type |
SRA |
| |
|
| Source name |
THP1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP1
cell type: monocyte cell line
shRNA: RUVBL2-specific inducible shRNA
agent: doxycycline
time point: day 2
|
| Treatment protocol |
TRIPZ-shRUVBL2 transduced THP1 cells were treated with either medium only or 1 μg/ml Doxycycline for 4 days.
|
| Growth protocol |
THP1 cells (monocyte cell line) (ATCC, Manassas, VA, USA) were maintained in culture in RPMI 1640 medium containing 10% fetal bovine serum, 100 units/ml penicillin and 100 ug/ml streptomycin at 37°C with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy Plus Mini Kit according to manufacturer's instructions.
Indexed RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA v2 protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
EAM204
processed data file: DAY2_NODOX_vs_DOX_fold_change.csv
|
| Data processing |
All tools in the analysis were invoked through the Galaxy Project for NGS analysis, as follows:
Fastq was demultiplexed and generated using Illumina bcl2fastq v2.19 before pre-processing (trimmomatic) to remove adapter read-through and poor quality sequences.
Pre-processed data were then aligned to the genome (UCSC hg38) with Bowtie 2 and deduplicated using Picard.
Reads-per-transcript were counted by FeatureCounts, before differential expression analysis by SARTools, a DESeq2 wrapper.
Genome_build: hg38
Supplementary_files_format_and_content: *_NODOX_vs_DOX_fold_change.csv: Comma-separated text files include average count values for each sample.
|
| |
|
| Submission date |
Jul 13, 2018 |
| Last update date |
Jan 01, 2019 |
| Contact name |
Owen Williams |
| E-mail(s) |
owen.williams@ucl.ac.uk
|
| Phone |
+4420790542180
|
| Organization name |
UCL GOS ICH
|
| Department |
Cancer section
|
| Street address |
30 Guilford Street
|
| City |
London |
| ZIP/Postal code |
WC1N 1EH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE117106 |
Gene expression changes in THP1 cells at day 2 and 4 following shRNA knock-down of RUVBL2 |
|
| Relations |
| BioSample |
SAMN09655841 |
| SRA |
SRX4390199 |
