|
| Status |
Public on Apr 22, 2024 |
| Title |
iTEC_10day_3 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse embryonic fibroblasts
cell type: iTECs
genotype: N/A
treatment: Cre-induced, 10 days
|
| Treatment protocol |
Primary iFoxn1/+ MEFs for Nucleofection experiment were passaged no more than 5 times for all analyses in this research. Nucleofection experiments were performed following the manufactures’ protocol for mouse embryonic fibroblasts: free program N-024 (Amaxa™ Nucleofector™, Lonza). To induce iFoxn1 expression, pPGK-Cre-bpA (Addgene # 11543) was used in the transfection according to the manufacturer’s protocol. After Nucleofection, cells were further cultured for 48 hours until sorted by flow cytometry.
|
| Growth protocol |
Primary iFoxn1/+ MEFs were thawed then cultured in DMEM containing 15% fetal calf serum, 2 mM sodium pyruvate, 4 mM glutamine, 50 µg/ml streptomycin and 50 U/ml penicillin (DMEM/FCS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the RNAeasy mini kit (Qiagen) according to the manufacturer’s instructions. All samples were DNaseI treated during the preparation.
RNA was frozen in -80'C freezer until the libraries could be constructed with UGA GGBC.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Bulk RNA sequencing was performed in Georgia genomics and bioinformatics core (GGBC) using an Illumina NextSeq 500 sequencing platform to generate single end sequencing data. Raw reads were pre-processed with sequencing grooming tools FASTQC, Trimmomatic and then further assembled by Hisat2, SAMtools, and StringTie. Differential gene expression analysis between samples and graphical display (including count matrix plot, PCA, heatmap and other plots) were performed using DEseq2 and R package ggplot2. Gene ontology enrichment analysis was performed using online EnrichR program (Chen et al.; Kuleshov et al.).
Assembly: mm10
Supplementary files format and content: Csv file containing a gene count matrix of all of the samples combined.
|
| |
|
| Submission date |
Apr 17, 2024 |
| Last update date |
May 16, 2024 |
| Contact name |
Seung Woo Kang |
| Organization name |
The University of Georgia
|
| Department |
Genetics
|
| Lab |
Manley Lab
|
| Street address |
500 D.W. Brooks Dr.
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE264265 |
MECHANISMS UNDERLYING THE DIRECT PROGRAMMING OF MOUSE EMBRYONIC FIBROBLASTS TO THYMIC EPITHELIAL CELLS BY FOXN1 [RNA-seq] |
|
| Relations |
| BioSample |
SAMN41054857 |
| SRA |
SRX24292566 |
