|
| Status |
Public on Nov 24, 2017 |
| Title |
Normal brain EC #2 |
| Sample type |
SRA |
| |
|
| Source name |
Normal brain EC
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue type: normal brain
cell type: Sorted Endothelial cell
|
| 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 |
| |
|
| 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 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
KANGSAN KIM |
| E-mail(s) |
Kangsan.kim@utsouthwestern.edu
|
| Phone |
+1-214-906-0923
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Pathology
|
| Lab |
Malladi Lab
|
| Street address |
5323 Harry Hines Blvd
|
| City |
DALLAS |
| State/province |
TX |
| ZIP/Postal code |
75290 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE90459 |
RNA-seq analysis of mouse brain endothelial cells and glioma endothelial cells |
|
| Relations |
| BioSample |
SAMN06050653 |
| SRA |
SRX2369855 |
