|
| Status |
Public on May 05, 2023 |
| Title |
CHO_EV_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MI5-4 (CHO)
|
| Organism |
Cricetulus griseus |
| Characteristics |
cell line: MI5-4 (CHO)
|
| Treatment protocol |
EV cells were treated 10 mM sodium lactate for 24 h.
|
| Growth protocol |
MI5-4 CHO cells were cultured in Minimum Essential Medium alpha containing 1,000 mg/L glucose supplemented with 10% fetal bovine serum and 1% penicillin‒streptomycin at 37 °C in a humidified atmosphere with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from MI5-4 CHO cells using a Direct-zol RNA MicroPrep Kit. The RNA purity, concentration, and integrity were evaluated with an Agilent TapeStation 4200.
RNA libraries were prepared using a Nugen Universal Plus mRNA-seq library preparation kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
EV_2
|
| Data processing |
Quality check was done using FastQC v0.11.8
Sequenced reads were trimmed using cutadapt v1.18, then mapped to CHOK1GS (Ensembl) using STAR v2.7.0a
Read counts were quantified by featureCount v2.0.1 and normalized to counts per million reads (CPM) using edgeR v3.8
Assembly: CHOK1GS
Supplementary files format and content: tab delimited-text file including CPM values from each sample
|
| |
|
| Submission date |
Apr 06, 2023 |
| Last update date |
May 05, 2023 |
| Contact name |
Nissim Hay |
| E-mail(s) |
nhay@uic.edu
|
| Organization name |
University of Illinois Chicago
|
| Department |
BMG
|
| Street address |
900 South Ashland Ave
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60607 |
| Country |
USA |
| |
|
| Platform ID |
GPL27425 |
| Series (2) |
| GSE229153 |
Hexokinase 2 and lactate mediated gene expression via histone H3 lysine 18 lactylation (CHO RNA-Seq) |
| GSE229156 |
Hexokinase 2 and lactate |
|
| Relations |
| SRA |
SRX19900043 |
| BioSample |
SAMN34105236 |
