|
| Status |
Public on Jul 27, 2016 |
| Title |
scr_p53_3 |
| Sample type |
SRA |
| |
|
| Source name |
HUVEC, si-p53
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human Umbilical Vein Endothelial Cells (HUVEC)
passages: 3
sirna treatment: si-p53
|
| Treatment protocol |
siRNA duplexes were transfected into subconfluent cells using RNAi Max and cells were collected for RNA extraction 48 hrs after transfection
|
| Growth protocol |
Primary Human Umbilical Vein Endothelial Cells were grown in EGM-2 media (Lonza)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and DNase treated using the Rneasy mini kit (Qiagen)
RNA and library preparation integrity were verified with a BioAnalyzer 2100 (Agilent) or LabChip Gx Touch 24 (Perkin Elmer). 2µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
si-p53
|
| Data processing |
Read quality trimming with Reaper 13-100 (-geom no-bc -3pa -clean-length 30 -qqq-check 53/20 -trim-length 150)
Mapping of reads versus human genome version GRCh37.p5 hg19 using STAR 2.4.0a (--outFilterMismatchNoverLmax 0.1)
Read counting per gene with featureCounts 1.4.5-p1 from the Subread package using default parameters
Differentially expressed genes were identified using DESeq2 version 1.62
Raw gene counts were normalized with DESeq
Genome_build: hg19
Supplementary_files_format_and_content: The tab-delimited text file (matrix.txt) contains DESeq normalized counts for all genes
|
| |
|
| Submission date |
Jul 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Oliver Andrew Stone |
| E-mail(s) |
oliver.stone@mpi-bn.mpg.de
|
| Phone |
+4960327051302
|
| Organization name |
Max Planck Institute
|
| Department |
Developmental Genetics
|
| Lab |
Stainier
|
| Street address |
Ludwigstr 43
|
| City |
Bad Nauheim |
| ZIP/Postal code |
61231 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE84877 |
Effect of from Human Umbilical Vein Endothelial Cells |
|
| Relations |
| BioSample |
SAMN05441502 |
| SRA |
SRX1978462 |
