|
| Status |
Public on Oct 25, 2021 |
| Title |
HUVECs senescent-3 |
| Sample type |
SRA |
| |
|
| Source name |
HUVECs
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: umbilical vein endothelial cells
condition: senescent
|
| Treatment protocol |
We prepared two kinds of HUVECs; one under proliferation as "young", the other that underwent replicative senescence as "senescent",
|
| Growth protocol |
Human umbilical vein endothelial cells(HUVECs) were cultured in Endothelial Cell Growth Medium-2(Lonza)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from young and senescent HUVECs using RNeasy Plus Micro Kit (Quiagen)
cDNA libraries were generated using a NEBNext Ultra RNA Library Prep Kit (New England BioLabs)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
HUVECs senescent-3
|
| Data processing |
libraries were analyzed on a Highseq1500(Illumina).
TopHat 2 (version 2.0.13) was used for mapping reads to the reference genome (Ensembl GRCh38/hg38) with annotation data downloaded from the Ensembl Asia website (URL https://asia.ensembl.org/).
Expression of each transcript was quantified as the number of fragments per kilobase of transcript per million fragments mapped (FPKM), and expression was compared among 3 groups by Cuffdiff (included in Cufflinks version 2.2.1).
Genome_build: Ensembl GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Aug 04, 2020 |
| Last update date |
Oct 25, 2021 |
| Contact name |
Goro Katsuumi |
| E-mail(s) |
g.katsuumi.qv@juntendo.ac.jp
|
| Organization name |
Juntendo University
|
| Street address |
Hongo 2-1-1
|
| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
111-8421 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE155680 |
RNA-seq analysis in young and senescent endothelial cells |
|
| Relations |
| BioSample |
SAMN15728525 |
| SRA |
SRX8884501 |
