|
| Status |
Public on Dec 02, 2019 |
| Title |
E98_KD |
| Sample type |
SRA |
| |
|
| Source name |
GLIOMA CELL LINE
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain
cell line: E98 glioma cell line
targeted with: p120-shRNA
|
| Treatment protocol |
Transient downregulation of adherens junction proteins and adhesion receptors was obtained for monolayer cultures on rBM using specific or matched non-targeting smart-pool RNAi (Dharmacon) or 5 individual RNA probes (Sigma). For stable downregulation of p120-catenin with lentiviral particles pLKO.1 (MISSION shRNA, Sigma)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen Rneasy Micro column based kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw reads mapped to human genome using GSNAP
Mapped reads were counted using HTSeq-count
raw counts was normalized using DESeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include DESeq normalized values for each Sample ...
All.normalised.raw.data.txt.gz: normalized raw data of all samples and replicas
U251_NT_KD.Downregulated.genes.xls.gz: Downregulated genes names and the corresponding GO terms
U251_NT_KD.Upregulated.genes.xls.gz: Upregulated genes and corresponding GO terms
E98_NT_KD.Downregulated.genes.xls.gz: Downregulated genes names and the corresponding GO terms
E98_NT_KD.Upregulated.genes.xls.gz: Upregulated genes and corresponding GO terms
E468_NT_KD.Downregulated.genes.xls.gz: Downregulated genes names and the corresponding GO terms
E468_NT_KD.Upregulated.genes.xls.gz: Upregulated genes and corresponding GO terms
|
| |
|
| Submission date |
Oct 14, 2015 |
| Last update date |
Dec 02, 2019 |
| Contact name |
Nader Atlasy |
| E-mail(s) |
[email protected]
|
| Organization name |
Radboud University
|
| Department |
Molecular Biology
|
| Lab |
Henk Stunnenberg
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| State/province |
Gerderland |
| ZIP/Postal code |
6500 HB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE73999 |
P120-catenin dependent glioma-cell networks drive growth and diffuse brain infiltration |
|
| Relations |
| BioSample |
SAMN04166231 |
| SRA |
SRX1334627 |
