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Sample GSM7659455 Query DataSets for GSM7659455
Status Public on Jun 11, 2024
Title MEFs_Ferroptotic_3
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 SAMN36698887
SRA SRX21144801

Supplementary file Size Download File type/resource
GSM7659455_Ferr-MEF-R3.txt.gz 192.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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