|
| Status |
Public on Mar 01, 2024 |
| Title |
H1 ESCs, MEK5DD.1 |
| Sample type |
SRA |
| |
|
| Source name |
H1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1
cell type: Human embryonic stem cells
genotype: MEK5DD overexpression
treatment: E8 medium
|
| Treatment protocol |
MAP2K5DD (MEK5DD) mutation (changed Ser311 to Asp, Ser315 to Asp) sequence was was subcloned into EZ-Lv195.1 cloning vector. MEK5DD-OE H1 ESC cell line was established after Lentiviral MAP2K5DD transduced in H1 ESCs and selected by puromycin.
|
| Growth protocol |
H1 ESCs was maintained in E8 medium supplemented with antibiotics with 5% CO2 at 37C. E8 medium contained DMEM/F12, sodium selenite, ascorbic acid trisodium, transferrin, insulin, FGF2 and TGFβ.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells was harvested in RNAiso Plus reagent (Takara). The poly(A) mRNA isolation was performed using Oligo(dT) beads according to manufacturer’s instructions
1 μg total RNA was used for following library preparation. The RNA Library were sequenced for paired end reads on Illumina NextSeq 500 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Quality control of RNA-seq raw data was performed using Trimmomatic version 0.36
RNA-seq clean data alignment was conducted using STAR version 020201 with the reference genome hg38.
All genes expression were quantified using FeatureCounts version 1.5.3
Differential expression genes (DEGs) were identified with the criteria of p adjusted value < 0.05 and the absolute value of log2(Fold Change) > 1 after profile normalized using DESeq2 version 1.26.0
DEGs analysis were performed the GO and KEGG enrichment analysis through the R package ClusterProfiler 4.0
|
| |
|
| Submission date |
Jun 02, 2023 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Chengcheng SONG |
| E-mail(s) |
chengchengsong2021@gmail.com
|
| Phone |
62167066
|
| Organization name |
university of macau
|
| Department |
fhs
|
| Street address |
universtiy of macau
|
| City |
macau |
| ZIP/Postal code |
999078 |
| Country |
Macau |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE234056 |
ERK5 sustains autocrine mitogenic balance for cell fate specification in human pluripotent stem cells [MEK4DD RNA-seq] |
| GSE234058 |
ERK5 sustains autocrine mitogenic balance for cell fate specification in human pluripotent stem cells |
|
| Relations |
| BioSample |
SAMN35573638 |
| SRA |
SRX20581134 |
