NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4160533 Query DataSets for GSM4160533
Status Public on Jan 07, 2020
Title RNA-seq_Adult_Brain_GFPpos_R2
Sample type SRA
 
Source name Adult GFP-positive sorted cells from brain
Organism Mus musculus
Characteristics strain/genotype: Tie2-GFP
age: Adult
Sex: Male
tissue: Brain
cell-type: Vascular endothelial cells
Growth protocol Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee
Extracted molecule total RNA
Extraction protocol For acutely isolated ECs, RNA was extracted from GFP-positive and GFP-negative cells that were FACS sorted directly into QIAGEN Buffer RLT Plus and then processed using the RNeasy Micro Plus kit (74034, QIAGEN, Venlo, Netherlands).
For RNA-seq, total RNA was converted to cDNA and amplified (Ovation Ultralow System V2-32, 0342HV, NuGEN Technologies, San Carlos, CA). Amplified cDNA was fragmented, end-repaired, linker-adapted, and single-end sequenced for 75 cycles on a NextSeq500 (Illumina Inc.). Cultured brain EC RNA-seq libraries were paired-end sequenced for 36 cycles on a NextSeq500.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Salmon version 0.14.0 (Patro et al., 2017) was used to quantify expression of transcripts from RNA-seq experiments using GENCODE release M21 (salmon quant -l A –validateMappings –mimicStrictBT2 --rangeFactorizationBins 4 --incompatPrior 0.0 --useVBOpt --seqBias --gcBias --posBias --biasSpeedSamp 10). To visualize RNA-seq data on an IGV browser (Robinson et al., 2011; Thorvaldsdóttir et al., 2013), HISAT2 version 2.1.0 (Kim et al., 2015) was used to generate alignment bam files (hisat2 --dta) and then deepTools was used to generate bigwig files (bamCoverage -bs 1 --normalizeUsing CPM).
Genome_build: mm10
 
Submission date Nov 14, 2019
Last update date Jan 07, 2020
Contact name Mark F Sabbagh
E-mail(s) msabbag2@jhmi.edu
Organization name Johns Hopkins University School of Medicine
Department Molecular Biology and Genetics
Lab Jeremy Nathans
Street address 725 North Wolfe Street
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platform ID GPL19057
Series (1)
GSE118731 A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture
Relations
BioSample SAMN13284246
SRA SRX7141263

Supplementary file Size Download File type/resource
GSM4160533_RNA-seq_Adult_Brain_GFPpos_R2_normalizedBigWig.bw 41.7 Mb (ftp)(http) BW
GSM4160533_RNA-seq_Adult_Brain_GFPpos_R2_salmon_output.sf.txt.gz 4.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap