|
| Status |
Public on Sep 15, 2022 |
| Title |
M_RNA_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Embryonic Fibroblast
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse Embryonic Fibroblast
treatment: Infected with Mef2c virus
|
| Treatment protocol |
MEF were infected with viruses encoding the reprogramming factors with polybrene(4ug/ml)
|
| Growth protocol |
Mice were raised and maintained under standard laboratory conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with TRIzol (Thermo Fisher) according to the manufacturer’s protocol.
Library preparation was performed with the Roche KAPA Stranded mRNA-Seq kit. Paired-end sequencing was performed on the NovaSeq SP platform to a depth of 4 X 107 reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Data quality was checked with FastQC and MultiQC.
Reads matching adapter sequences or with a mean quality score less than 20 were trimmed with Bbduk. Pseudoalignment was performed with Salmon using the mm10 cDNA transcriptome as reference.
Differential gene expression analysis was performed with DESeq2. Genes with an adjusted p value less than 0.1 and an absolute fold change greater than 1.5 compared to the relevant control.
Genome_build: mm10 reference
Supplementary_files_format_and_content: 1 csv files containg tpm of Ascl1, Mef2c, and H3K27ac Peaks of A, M, and AM infected fibroblast in replicates
|
| |
|
| Submission date |
Dec 29, 2021 |
| Last update date |
Sep 15, 2022 |
| Contact name |
LI QIAN |
| E-mail(s) |
li_qian@med.unc.edu
|
| Phone |
919 9624982
|
| Organization name |
UNC
|
| Department |
Department of pathology
|
| Lab |
Qian Lab
|
| Street address |
111 Mason Farm Road, MBRB
|
| City |
Chapel Hill |
| ZIP/Postal code |
27517 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE192729 |
Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [RNA-seq I] |
| GSE192788 |
Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes |
|
| Relations |
| BioSample |
SAMN24492157 |
| SRA |
SRX13548495 |
