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Sample GSM4216372 Query DataSets for GSM4216372
Status Public on Jun 01, 2020
Title cage_275887_pup4_KO
Sample type SRA
Source name P6 brain FACS isolated mouse endothelial cells
Organism Mus musculus
Characteristics cell type: Brain endothelial cells
passages: primary uncultured endothelial cells
strain: C57BL/6
age: post natal day 6
genotype: GLUT1EC-/-
Growth protocol Brain endothelial cells were isolated from GLUT1EC-/- mice and WT littermates using FACS sorting from neonates (P6). ECs were sorted directly into RLT plus RNeasy plus lysis buffer.
Extracted molecule total RNA
Extraction protocol RNA was extracted using RNeasy Plus Micro Kit (Cat No. 74034, Qiagen, Hilden, Germany). RNA was stored in -80 freezer till further processing for RNA-sequencing.
The libraries were prepared following Illumina TruSeq stranded mRNA protocol. The quality of the RNA and final libraries was determined using an Agilent 4200 TapeStation System. The libraries were pooled equimolecularly and sequenced in an Illumina NovaSeq sequencer (single-end 100 bp) with a depth of around 20 Mio reads per sample.
Illumina TruSeq stranded mRNA protocol
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Data processing Reads were aligned with STAR aligner with the options --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Alignments were counted with the featureCounts function
Genome_build: GRCm38
Supplementary_files_format_and_content: text files holding match counts per gene
Submission date Dec 12, 2019
Last update date Jun 02, 2020
Contact name Katrien De Bock
Organization name ETH Zurich
Department D-HEST
Lab Lab of Exercise and Health
Street address Schorenstrasse 16
City Schwerzenbach
State/province Z├╝rich
ZIP/Postal code 8603
Country Switzerland
Platform ID GPL21103
Series (2)
GSE141924 Transcriptome analysis of brain endothelial cells from EC-specific Glut1 knock-out pups (P6) as compared to wild type controls
GSE141926 Transcriptome analysis of brain endothelial cells from EC-specific Glut1 knock-out mice
BioSample SAMN13547588
SRA SRX7354558

Supplementary file Size Download File type/resource
GSM4216372_cage_275887_pup4_KO.txt.gz 124.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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