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Sample GSM4094683 Query DataSets for GSM4094683
Status Public on Sep 25, 2019
Title WT2
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
City Beijing
ZIP/Postal code 100089
Country China
 
Platform ID GPL24247
Series (1)
GSE137942 Genome-wide maps of chromatin state in 5-HT6R knock out mice.
Relations
BioSample SAMN12830885
SRA SRX6896273

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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