|
| Status |
Public on Jan 09, 2024 |
| Title |
B3 |
| Sample type |
SRA |
| |
|
| Source name |
esophagus mucosa
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: esophagus mucosa
cell line: Eca-109
cell type: esophageal squamous cell carcinoma cells
treatment: treated with siMOF-1
|
| Treatment protocol |
transfected with siRNA
|
| Growth protocol |
RPM1640,10%FBS,1%Antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent.
Briefly, libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, E7530)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw data (fastq) were processed using in-house perl scripts to remove any remaining adaptors and ambiguous nucleotides.
The trimmed sequence files were mapped to the reference genome, Homo Sapiens (GRCh38/hg38), using HISAT2 (v2.0.5).
Gene expression levels were quantified as Fragments Per Kilobase of transcript per Millions base pairs sequenced.
Differential expression analysis of MOF knockdown (si-MOF#1, si-MOF#2) and control (si-NC) groups was performed using DESeq2 R package (1.16.1).
Differentially expressed genes (DEGs) were identified according to the criteria of |log2(foldchange)| ≥1 and adjusted P value < 0.05. Finally, GO enrichment analysis for 430 shared DEGs was performed using the analysis tool NovoMagic by Novogene.
Assembly: Homo Sapiens (GRCh38/hg38)
Supplementary files format and content: Tab-delimited text file inckude raw counts for each sample
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Aug 17, 2023 |
| Last update date |
Jan 09, 2024 |
| Contact name |
Peichao Li |
| E-mail(s) |
[email protected]
|
| Phone |
13705454987
|
| Organization name |
Shandong University
|
| Department |
thoracic surgery department
|
| Lab |
Key Laboratory of Thoracic Oncology
|
| Street address |
The Second Hospital of Shandong University
|
| City |
Jinan |
| State/province |
Shangdong |
| ZIP/Postal code |
250012 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE241066 |
USP10-mediated MOF (KAT8) stabilization accelerates the malignant progression of esophageal squamous cell carcinoma via epigenetically activating of ANXA2/Wnt signaling |
|
| Relations |
| BioSample |
SAMN37021096 |
| SRA |
SRX21388817 |
