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Sample GSM3935336

Query DataSets for GSM3935336

Status

Public on Jul 01, 2020

Title

m1_AY_Y3_L2

Sample type

SRA

Source name

three-mo mouse BEC

Organism

Mus musculus

Characteristics

cell type: primary murine brain endothelial cells

Growth protocol

Mice 3 (young)

Extracted molecule

total RNA

Extraction protocol

Brain tissues were dissected using Miltenyi neural dissociation kit. Brain endothelial cells were isolated via FACS.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: raw count table

Submission date

Jul 09, 2019

Last update date

Jul 01, 2020

Contact name

Michelle Berkeley Chen

E-mail(s)

[email protected]

Organization name

Stanford

Street address

318 Campus Drive