|
| Status |
Public on Jun 24, 2024 |
| Title |
MEF 2# |
| Sample type |
SRA |
| |
|
| Source name |
MEF
|
| Organism |
Mus musculus |
| Characteristics |
cell line: MEF
cell type: mouse embryonic fibroblast
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using FreeZol reagent (Vazyme),1 µg of RNA was used for sequencing libraries construction
Liarbries were constructed by VAHTS mRNA-seq v3 Library Prep Kit for Illumina (NR611, Vazyme)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
iPSC_Transcript_fpkm.txt
GeneSymbol_fpkm.txt
|
| Data processing |
The RNA-seq reads were trimmed using Trim Galore (v0.6.4) and then mapped to the mm10 reference genome with HISAT2 (v2.2.1) , and StringTie (v2.2.1) was used to quantify the transcription level of each gene in each sample into FPKM (Fragments per kilobase of exon model per million mapped reads). GFOLD (v1.1.4) was used to perform differential expression analysis between conditions. The differentially expressed genes were identified with gfold value > 0.5.
Assembly: mm10
Supplementary files format and content: expression matrix(FPKM)
|
| |
|
| Submission date |
Sep 19, 2023 |
| Last update date |
Jun 24, 2024 |
| Contact name |
Chengchen Zhao |
| E-mail(s) |
zhaochengchen@westlake.edu.cn
|
| Organization name |
Westlake University
|
| Lab |
Laboratory of Cell Fate Control
|
| Street address |
Dunyu Road No.600, Xihu District
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310030 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE243516 |
Rational cell fate engineering through chromatin dynamics [RNA-Seq] |
| GSE243517 |
Rational cell fate engineering through chromatin dynamics |
|
| Relations |
| BioSample |
SAMN37452924 |
| SRA |
SRX21820774 |
