|
Status |
Public on Jul 27, 2016 |
Title |
pkm2_p53_1 |
Sample type |
SRA |
|
|
Source name |
HUVEC, si-PKM2 and sip53
|
Organism |
Homo sapiens |
Characteristics |
tissue: Human Umbilical Vein Endothelial Cells (HUVEC) passages: 3 sirna treatment: si-PKM2 and sip53
|
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-PKM2 and sip53
|
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 |
SAMN05441498 |
SRA |
SRX1978466 |