|
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 |