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Status |
Public on Jan 07, 2020 |
Title |
RNA-seq_Adult_Brain_GFPpos_R2 |
Sample type |
SRA |
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Source name |
Adult GFP-positive sorted cells from brain
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Organism |
Mus musculus |
Characteristics |
strain/genotype: Tie2-GFP age: Adult Sex: Male tissue: Brain cell-type: Vascular endothelial cells
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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
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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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
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Submission date |
Nov 14, 2019 |
Last update date |
Jan 07, 2020 |
Contact name |
Mark F Sabbagh |
E-mail(s) |
msabbag2@jhmi.edu
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Organization name |
Johns Hopkins University School of Medicine
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Department |
Molecular Biology and Genetics
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Lab |
Jeremy Nathans
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Street address |
725 North Wolfe Street
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City |
Baltimore |
State/province |
MD |
ZIP/Postal code |
21205 |
Country |
USA |
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Platform ID |
GPL19057 |
Series (1) |
GSE118731 |
A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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