|
| Status |
Public on May 07, 2019 |
| Title |
siSCR_9 [WGC100685R] |
| Sample type |
SRA |
| |
|
| Source name |
HUVEC_siSCR
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human umbilical vein endothelial cells (HUVEC)
genotype/variation: siSCR
|
| Treatment protocol |
siRNAs were purchased from Qiagen: siRNA MAPK1_10 and MAPK3_6, and siSCR #1027281. siRNA transfetions were done in OptiMem medium (ThermoFisher) with the lipofectamine RNAimax transfection agent (ThermoFisher).
|
| Growth protocol |
Human Umbilical Vein Endothelial Cells (HUVEC) were purchased from Lonza and cultivated in EBM-2 MV medium (Lonza)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extractions were done using RNeasy mini kit (Qiagen) with DNAse digestion (Qiagen).
Paired-end sequencing library was prepared using Illumina Truseq v1 library prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
WGC100685R_combined
|
| Data processing |
Bases were called in real-time on the Illumina HiSeq X
Paired-end reads were aligned to hg38 (GRCh38) using STAR 2.5.1b aligner with a custom-built index in two-pass mode. The first pass parameters were: --twopassMode Basic --outFilterType BySJout --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.66 --outFilterIntronMotifs None --outSJfilterReads All --outSAMstrandField intronMotif --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 0 --chimScoreDropMax 20 --chimScoreSeparation 10 --chimScoreJunctionNonGTAG -1 --quantMode TranscriptomeSAM. The second pass genome index was created from the first pass SJ.out.tab file with an --sjdbOverhang 149. The second pass alignment was run against the new index, with the same initial alignment parameters.
Expression quantification was performed using RSEM v1.2.28 with GENCODE release 24 annotation using the following parameters: --bam --no-bam-output --estimate-rspd --append-names --paired-end --forward-prob 0.5
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file including RSEM counts for each sample
|
| |
|
| Submission date |
May 06, 2019 |
| Last update date |
May 07, 2019 |
| Contact name |
Nicolas Ricard |
| E-mail(s) |
nic.ricard@gmail.com
|
| Phone |
2036062009
|
| Organization name |
yale university
|
| Department |
internal medicine
|
| Lab |
Michael Simons
|
| Street address |
300 george street
|
| City |
new haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE130737 |
Endothelial ERK1/2 signaling maintains integrity of the quiescent endothelium |
|
| Relations |
| BioSample |
SAMN11580922 |
| SRA |
SRX5795144 |
