|
| Status |
Public on Apr 27, 2020 |
| Title |
shMOB2 |
| Sample type |
SRA |
| |
|
| Source name |
LN-229 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: epithelial glioma cells
passages: 15-18
tissue: brain
|
| Treatment protocol |
LN-229 cells were infected with pGIPZ-CTRL and MOB2-shRNA lentiviruses, and stable clones were selected using puromycin.
|
| Growth protocol |
Cells were routinely generated by re-plating with DMEM supplied with 5% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from LN-229-shMOB2 or LN-229-shControl cells using TRIzol Reagent.
The sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
clean reads were retained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw fastq data using in-house perl scripts
RNASeq reads were aligned to the hg38 genome assembly using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to generate gene-level count matrix as input for edgeR’s statistical model
Differential expression analysis between shFKBP9 and shControl cells was performed using the edgeR package
Genome_build: hg38
Supplementary_files_format_and_content: Excel file include FPKM expression value and gene annotation
|
| |
|
| Submission date |
Oct 24, 2019 |
| Last update date |
Apr 27, 2020 |
| Contact name |
Ke Jiang |
| Organization name |
Dalian Medical University
|
| Street address |
lvshun south road no.9
|
| City |
Dalian |
| State/province |
Liaoning |
| ZIP/Postal code |
116044 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE139339 |
RNA sequencing analysis of LN-229-shControl and LN-229-shMOB2 cells |
|
| Relations |
| BioSample |
SAMN13108587 |
| SRA |
SRX7052198 |
