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Sample GSM3852175 Query DataSets for GSM3852175
Status Public on Dec 31, 2019
Title circRNA AD2_6m
Sample type SRA
Source name brain
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: brain
age: 6-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
Organization name peking university
Street address haidian
ZIP/Postal code 100000
Country China
Platform ID GPL21273
Series (1)
GSE132177 A systematic dissection of whole transcriptome profiling in the APP/PS1 mouse brain
BioSample SAMN11958501
SRA SRX5972713

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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