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Sample GSM8728960 Query DataSets for GSM8728960
Status Public on Jan 16, 2025
Title KO1
Sample type SRA
 
Source name liver
Organism Mus musculus
Characteristics tissue: liver
genotype: ZUP1 knock-out
treatment: MHV infection
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Trizol reagent (Invitrogen) and reverse transcribed into cDNA with GoScriptTM Reverse Transcription System (Promega). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Library name: Sample 1
Data processing Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
 
Submission date Jan 13, 2025
Last update date Jan 16, 2025
Contact name HAO wenyan
Organization name Peking University Health Science Center
Department School of Basic Medical Sciences
Street address P.R.
City BEIJING
ZIP/Postal code 100191
Country China
 
Platform ID GPL24247
Series (1)
GSE286528 Gene expression differences between wild-type and ZUP1 knock-out mice in liver infected with MHV-A59
Relations
BioSample SAMN46231940
SRA SRX27334590

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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