|
| Status |
Public on Jan 27, 2018 |
| Title |
Sox7 ECKO-2 |
| Sample type |
SRA |
| |
|
| Source name |
endothelial cells from high grade glioma
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Sox7-deficient
cell type: endothelial cells from high grade glioma
|
| Growth protocol |
housed in a pathogen-free animal facility
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
2-S7-ECKO-170110
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
Nov 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Chan Soon Park |
| E-mail(s) |
parkcs87@gmail.com
|
| Organization name |
KAIST
|
| Department |
graduate school of medical science and engineering
|
| Lab |
VBS
|
| Street address |
291 Daehak-ro, Yu-seong gu
|
| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE107530 |
RNA analysis of Sox7- and Sox17-deficient mouse endothelial cells from high grade glioma |
|
| Relations |
| BioSample |
SAMN08113836 |
| SRA |
SRX3433160 |
