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| Status |
Public on Nov 02, 2015 |
| Title |
HUVEC_Control_2 |
| Sample type |
SRA |
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| Source name |
HUVEC (Human umbilical vein vascular endothelial cells), replicate 2
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Human umbilical vein vascular endothelial cells
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| 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.
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| 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).
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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
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| Submission date |
Jul 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Fang Liu |
| E-mail(s) |
liufangphd@163.com
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| Organization name |
center hospital affiliated to Shenyang medical college
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| Department |
Department of Neurology
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| Street address |
Nanqi west road no.5
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| City |
Shenyang |
| State/province |
Liaoning |
| ZIP/Postal code |
110024 |
| Country |
China |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE71216 |
Transcriptome sequencing to identify transcription factor regulatory network and alternative splicing in endothelial cells under VEGF stimulation |
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| Relations |
| Reanalyzed by |
GSE81474 |
| BioSample |
SAMN03893403 |
| SRA |
SRX1115727 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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