|
| Status |
Public on Jun 11, 2024 |
| Title |
MEFs_Ferroptotic_1 |
| Sample type |
SRA |
| |
|
| Source name |
Bach1-/- pMEFs
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Bach1-/- pMEFs
cell type: Mouse embryonic fibroblasts
genotype: Bach1 knockout
treatment: Cultured in ferroptotic-cells-derived medium
|
| Treatment protocol |
Hepa1 cells and Bach1-/- pMEFs were cultured in the medium derived from control or ferroptotic iMEFs for totally 4 days. 2-ME (0.1mM) and vitamin.E (0.4 mg/mL) were added to the medium.
The culture medium was replaced daily with a new one derived from control or ferroptotic iMEFs.
|
| Growth protocol |
Control or Bach1-re-expressed (ferroptotic) immortalized MEFs (iMEFs) were cultured in DMEM including 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, 1% nonessential amino acids for 48 h. The supernatant medium was used for the following culture of Hepa1 or Bach1-/- primary MEFs (pMEFs).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy plus mini kit (Qiagen).
Libraries for RNA-seq were prepared from 100 ng of total RNA using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) with the protocol described in the manufacturer’s manual.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Quality of the reads was evaluated with FastQC (v0.11.9).
Sequence reads were trimmed for low quality sequence using Trimmomatic (v0.39).
Trimmed sequence reads were mapped to GRCm38/mm10 using STAR (2.7.10a).
Read count extraction was performed using HTSeq (v0.9.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
|
| |
|
| Submission date |
Jul 24, 2023 |
| Last update date |
Jun 11, 2024 |
| Contact name |
Hironari Nishizawa |
| E-mail(s) |
hnishizawa@med.tohoku.ac.jp
|
| Organization name |
Tohoku University Graduate School of Medicine
|
| Department |
Department of Biochemistry
|
| Street address |
2-1 Seiryo-machi, Aoba-ku
|
| City |
Sendai |
| ZIP/Postal code |
980-8575 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE238147 |
BACH1 suppresses cellular senescence, obesity, and short lifespan by ferroptotic FGF21 secretion |
|
| Relations |
| BioSample |
SAMN36698889 |
| SRA |
SRX21144799 |
