|
| Status |
Public on Jun 29, 2024 |
| Title |
HUVECs treated with 5 mM of L-glucose for 6 hours under hypxia/serum starvation conditions 2 |
| Sample type |
SRA |
| |
|
| Source name |
Human umbilical vein endothelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human umbilical vein endothelial cells
genotype: wild type
treatment: L-Glucose
|
| Treatment protocol |
HUVECs were treated with L-Glucose (5 mM) vs. glucosamine (5 mM) for 6 hours under 2% hypoxia and serum starvation
|
| Growth protocol |
HUVECs were endothelial cell growth media (cell application 211-500) in 37 degrees celisius in CO2 incubator
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Direct-zol RNA MiniPrep, Cat.No: R2052, 800 ng of total RNA was used for the construction of sequencing libraries.
ORNA libraries for RNA-sea were prepared using SMARTER mRNA-Seq Library Prep Kit flowing manufacture's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
FASTASeq 300 |
| |
|
| Data processing |
The BCL files were demultiplexed and converted to FASTQ format with bcl2fastq2 (v2.20.0).FastQC(v0.12.1) was used to evaluate reads quality. Reads were aligned to the reference genome (GENCODE:GRCh38.p13) usingSTAR(v2.7.10b) aligner. HTSeq-counts was used to count reads for each gene. Differential expression analysis was done usingDESeq2package. Also, theapeglmpackage was used for effect size estimation and lfcShrink log2 fold-change values.
Assembly: GENCODE:GRCh38.p13
Supplementary files format and content: processed data files format and content tab-delimited text file includes raw counts for each Sample The complete results of DE analysis is in DE_Analysis_Results.csv file.
|
| |
|
| Submission date |
Jun 24, 2024 |
| Last update date |
Jun 29, 2024 |
| Contact name |
Suhib Alhusban |
| E-mail(s) |
salhusban@augusta.edu
|
| Phone |
6156383454
|
| Organization name |
Augusta university
|
| Department |
VBC
|
| Street address |
1120 15th Street
|
| City |
Augusta |
| State/province |
Georgia |
| ZIP/Postal code |
30912-3800 |
| Country |
USA |
| |
|
| Platform ID |
GPL34633 |
| Series (1) |
| GSE270552 |
Glucosamine Mediated Hexosamine Biosynthesis Pathway Activation Utilizes ATF4 to Promote “Exercise-Like” Angiogenesis and Perfusion Recovery in Peripheral Arterial Disease |
|
| Relations |
| BioSample |
SAMN42048003 |
| SRA |
SRX25059268 |
