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Sample GSM3852190

Query DataSets for GSM3852190

Status

Public on Dec 31, 2019

Title

circRNA AD1_9m

Sample type

SRA

Source name

brain

Organism

Mus musculus

Characteristics

strain: C57BL/6
tissue: brain
age: 9-month-old
genotype: APP/PS1

Treatment protocol

The details of mRNA-seq, miRNA-seq, and circRNA-seq methods are described in Supplementary files.

Extracted molecule

total RNA

Extraction protocol

Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

ncRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

HiSeq X Ten

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: mm8
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

Submission date

Jun 04, 2019

Last update date

Dec 31, 2019

Contact name

MA NA NA

E-mail(s)

15176888063@163.com

Organization name

peking university

Street address

haidian