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Sample GSM2401526 Query DataSets for GSM2401526
Status Public on Nov 24, 2017
Title Glioma EC #1
Sample type SRA
Source name Glioma EC
Organism Mus musculus
Characteristics strain: C57BL/6
tissue type: Glioma (3weeks after orthotopic injection)
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
Phone +1-214-906-0923
Organization name UT Southwestern Medical Center
Department Pathology
Lab Malladi Lab
Street address 5323 Harry Hines Blvd
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
BioSample SAMN06050651
SRA SRX2369857

Supplementary file Size Download File type/resource
GSM2401526_Glioma-ECS_0121.txt.gz 111.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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