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Sample GSM1830135 Query DataSets for GSM1830135
Status Public on Nov 02, 2015
Title HUVEC_Control_2
Sample type SRA
 
Source name HUVEC (Human umbilical vein vascular endothelial cells), replicate 2
Organism Homo sapiens
Characteristics cell type: Human umbilical vein vascular endothelial cells
Treatment protocol The 3th generation of HUVECs were inoculated on 60 mm plate (2×105 cells/plate) and incubated for 1 day. For the VEGF group (2 samples), vascular endothelial growth factor 165 (VEGF165; PeproTech, Rocky Hill, NJ, USA) dissolved in medium 1640 was then added (final concentration based on pre-experiment: 16 ng/mL). In contrast, for the control group (2 samples), only medium 1640 was added with the same volume.
Growth protocol HUVECs were obtained from Cell Bank at the Chinese Academy of Sciences and incubated in medium 1640 (Life technologies, Gaithersburg, MD, USA) plus fetal bovine serum (FBS; Gibco, UK; 10% (v/v)), penicillin (Gibco, UK; 100 U/ml), streptomycin (Gibco, UK; 100 µg/ml), and endothelial cell growth supplements (ECGS; R&D Systems, Minneapolis, MN, USA), at 37°C in 5% CO2 humidified incubator (Thermo Labsystems, Vantaa, Finland).
Extracted molecule total RNA
Extraction protocol RNA were extracted by using Trizol agent (Invitrogen, Carlsbad, CA). RNA integrity was validated by using 2% agarose gel electrophoresis with Agilent 2100 Bioanalyzer, and RNA purity were verified based on absorbance (Abs) at 260 and 280 nm (Abs260/Abs280 > 1.8).
cDNA library was constructed according to the standard protocol of NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (Invitrogen, Carlsbad, CA), and then, cDNAs were amplified by using polymerase chain reaction for 12 cycles. The amplified cDNA library was sequenced by utilizing Illumina HiSeq™ 2500 sequencer (Illumina, San Diego, CA, USA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Illumina Casava1.7 software used for basecalling.
low quality sequences were filtered by NGSQC Toolkit, then mapped to hg19 by tophat2 with parameters -p 4 --no-mixed.
FPKM (expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced) were calculated using Cuffdiff.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
 
Submission date Jul 22, 2015
Last update date May 15, 2019
Contact name Fang Liu
E-mail(s) liufangphd@163.com
Organization name center hospital affiliated to Shenyang medical college
Department Department of Neurology
Street address Nanqi west road no.5
City Shenyang
State/province Liaoning
ZIP/Postal code 110024
Country China
 
Platform ID GPL16791
Series (1)
GSE71216 Transcriptome sequencing to identify transcription factor regulatory network and alternative splicing in endothelial cells under VEGF stimulation
Relations
Reanalyzed by GSE81474
BioSample SAMN03893403
SRA SRX1115727

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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