|
| Status |
Public on Mar 19, 2014 |
| Title |
HUVEC rep1 |
| Sample type |
SRA |
| |
|
| Source name |
human umbilical vein endothelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HUVEC (human umbilical vein endothelial cells)
source: multiple donors
|
| Treatment protocol |
Cells were cultivated in EGM medium, containing 10% FCS (Lonza)
|
| Growth protocol |
Third passage HUVEC (bought from Lonza, Basel, Switzerland)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated with the miRNeasy kit from Qiagen
Illumina TruSeq RNA sample preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
fastq-multx -B barcode_withA.txt -b -m 0 lane1_phred33.fastq -o demultiplexed/%.fastq
tophat2 -p 8 -N 2 --read-edit-dist 2 -o tophat_ctrl1 -G ../../../../databases/human/hg19/lncRnas/Noncode_UCSC.gtf /media/media/databases/human/hg19/hg19_refGenome_UCSC HUVEC.fastq
cufflinks -p 6 -o cufflinks_ctr1/ -G /media/media/databases/mouse/hg19/Homo_sapiens.GRCh37.68_ENSEMBLE.gtf -u -b /media/media/databases/mouse/hg19/hg19.fa ../tophat_HUVEC/accepted_hits.bam
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
|
| |
|
| Submission date |
Jan 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Reinier Boon |
| Organization name |
Amsterdam UMC
|
| Street address |
De Boelelaan 1117
|
| City |
Amsterdam |
| ZIP/Postal code |
1081 HV |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE54384 |
Human endothelial polyA+ RNA expression analysis |
|
| Relations |
| BioSample |
SAMN02595999 |
| SRA |
SRX449097 |
