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Sample GSM2040945 Query DataSets for GSM2040945
Status Public on Mar 30, 2016
Title RNAseq_prePHX_KO_rep1
Sample type SRA
Source name frozen pre-hepatectomy liver tissue
Organism Mus musculus
Characteristics strain: C57/B6 and 129 mix
tissue: liver
age: postnatal day 90
genotype: Arid1a Fl/Fl; Alb-cre
Treatment protocol The mice were performed for two thirds partial hepatectomy and 40 hours later sack mice.Liver tissues were collected and frozen in -80.
Extracted molecule total RNA
Extraction protocol Frozen liver tissues RNA was harvested using Trizol reagent and the Qiagen miRNeasy Mini kit.
RNA libraries were prepared for sequencing using standard Illumina or Nugen library protocols.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Sequence reads were aligned to mouse genome version mm9(pre-phx) and mm10(post-phx) using TopHat.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit RPKM (number of reads per kilo base pair per million total reads)
Differential gene expression analyses were performed using edgeR.
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: text file of gene RPKM values
Submission date Jan 15, 2016
Last update date May 15, 2019
Contact name Xuxu Sun
Organization name shanghai jiao tong university
Department school of medicine
Street address 227 south chongqing road
City shanghai
ZIP/Postal code 200025
Country China
Platform ID GPL17021
Series (2)
GSE76926 RNA-seq transcriptonal profiling in partial hepatectomy liver tissues in Arid1a WT and liver specific KO mice.
GSE76935 Suppression of SWI/SNF component Arid1a promotes mammalian regeneration through chromatin remodeling
BioSample SAMN04417786
SRA SRX1532680

Supplementary file Size Download File type/resource
GSM2040945_lane6_XSf2_1_RNA-Seq.xls.gz 3.1 Mb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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