|
| Status |
Public on Dec 04, 2022 |
| Title |
HUVEC, VEGF, STAT3 siRNA, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Human umbilical vein endothelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human umbilical vein endothelial cells (HUVECs)
treatment: 25 ng/mL VEGF for 24h
transfection: STAT3 siRNA
genotype: STAT3 knockdown
|
| Treatment protocol |
Cells were stimulated for 24h by cytokines. The following concentrations were used: VEGF (25 ng/mL), OSM+VEGF (100 ng/mL + 25 ng/mL), CNTF+CNTFR+VEGF (100 ng/mL + 200 ng/mL + 25 ng/mL)
|
| Growth protocol |
HUVECs (Cat#: C2519A, Lonza Group) were transfected with 15 nM STAT3 siRNA (Cat#: 1299001, siRNA ID: VHS40491 Thermo Fisher Scientific) or 15 nM Control siRNA (Cat#: 12935300, Thermo Fisher Scientific) for 6h and incubated in medium for additional 42h.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Qiazol (Cat#: 79306, Qiagen) and RNeasy Micro Kit (Cat#: 74004, Qiagen) was used for RNA extraction
Librarys were generated by Illumina TruSeq Stranded mRNA Sample Preparation Guide (Cat#: 20020594, Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.6.14. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software.
STAR aligner (Galaxy Version 2.7.5b) for mapping using standard settings
Merging BAM Files of Flow Cell 1 and 2
featureCounts (Galaxy Version 1.6.4) for generating count matrix using standard settings
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files with counts generated by featureCounts and corresponding Ensembl Stable IDs
|
| |
|
| Submission date |
Mar 11, 2022 |
| Last update date |
Dec 04, 2022 |
| Contact name |
Julian Rapp |
| E-mail(s) |
julian.rapp.work@gmail.com
|
| Organization name |
University Medical Center Freiburg
|
| Street address |
Killianstraße 5
|
| City |
Freiburg im Breisgau |
| ZIP/Postal code |
79106 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE198484 |
RNA sequencing of HUVECs stimulated with VEGF, OSM+VEGF, or CNTF+CNTFR+VEGF with or without STAT3 knock-down |
|
| Relations |
| BioSample |
SAMN26586461 |
| SRA |
SRX14445220 |
