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Sample GSM4094682

Query DataSets for GSM4094682

Status

Public on Sep 25, 2019

Title

WT1

Sample type

SRA

Source name

Hiipocampus

Organism

Mus musculus

Characteristics

strain: C57BL/6
tissue: Hiipocampus
age: post natal day 90
genotype: Wild type

Extracted molecule

total RNA

Extraction protocol

Total RNA was isolated from freshly dissected tissue using the TRNzol Reagent kit (TIANGEN, DP405) according to the manufacturer instructions. NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530L) 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

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

Submission date

Sep 24, 2019

Last update date

Sep 26, 2019

Contact name

Bingjie Wang

E-mail(s)

bingjiewang@pku.edu.cn

Organization name

Peking University

Street address

Yiheyuan ROAD 5