|
| Status |
Public on Sep 25, 2020 |
| Title |
HeLa cells, siEXT1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
treatment: siEXT1
genotype: knockdown of EXT1
|
| Treatment protocol |
HeLa cells were transfected with siCTRL, siEXT1 or siFBXW7, with Calcium Phosphate using ProFection Mammalian Transfection kit from Promega according to manufacturer’s instructions on cells cultured in DMEM at 40-50% confluence. Medium was changed 24 hours later and cells were collected 48h post-transfection.
|
| Growth protocol |
HeLa cells were cultured in in DMEM supplemented with 10% fetal bovine serum (FBS), 2mM glutamine and penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using GeneJET RNA Purification Kit (Thermo scientific), quantified and tested for RNA quality controlled using Agilent 2100 bioanalyzer using the Eukaryote Total RNA Nano assay.
Total RNA strands were used to generate libraries and sequenced by HiSeq2000 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were mapped to the human genome (GRCh 37/hg19) using BWA version 0.6 (Li and Durbin, 2009).
We used SWEMBL version 3.3.1 (http://www.ebi.ac.uk/~swilder/SWEMBL/) to identify the peaks. We adjusted parameters for RNA-seq and reference (Input) sequence relative to the number of reads in the samples, with a relative gradient of 0.002 (R parameter)
The peaks were submitted to GREAT version 2.0.2 to annotate nearest genes (minimum distance of 5.0 kb upstream and 1.0 kb downstream of the transcription start sites, up to 1000.0 kb maximum extension).
Genome_build: hg19
Supplementary_files_format_and_content: .xlsx
|
| |
|
| Submission date |
Sep 25, 2019 |
| Last update date |
Sep 25, 2020 |
| Contact name |
Jean-Claude Twizere |
| E-mail(s) |
jean-claude.twizere@uliege.be
|
| Phone |
+3243669981
|
| Organization name |
GIGA Institute
|
| Department |
Molecular Biology of Diseases
|
| Lab |
Viral Interactomes Lab
|
| Street address |
CHU - B34 Quartier Hôpital Avenue de l'Hôpital,11
|
| City |
Liège |
| State/province |
Liège |
| ZIP/Postal code |
4000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE138030 |
Transcriptome analysis of HeLa cells knocked down for EXT1 or FBXW7 gene expression |
|
| Relations |
| BioSample |
SAMN12854544 |
| SRA |
SRX6907627 |
