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Sample GSM1067319 Query DataSets for GSM1067319
Status Public on Jul 12, 2014
Title control cycling 2
Sample type SRA
Source name liver
Organism Mus musculus
Characteristics tissue: liver
genotype: cTKO
cell cycle state: cycling
treatment: 36 hrs after 2/3rd partial hepatectomy
Extracted molecule total RNA
Extraction protocol Livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared and sequencing was performed by Centrillion Biosciences
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing Illumina HiSeq 2000 was used to run the samples.
Sequenced reads were trimmed for adapter sequences then mapped to mm10 whole genome using tophatv2.0.0 and the down stream analysis is prformed using cufflinks v1.3.0
Fragments 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
Supplementary_files_format_and_content: FPKM tracking file include FPKM values
Submission date Jan 18, 2013
Last update date May 15, 2019
Contact name Julien Sage
Phone (650) 723-5113
Organization name Stanford University
Department Pediatrics
Lab Sage
Street address 265 Campus Drive, SIM1 G2078
City Stanford
State/province CA
ZIP/Postal code 94305-5457
Country USA
Platform ID GPL13112
Series (1)
GSE43631 next generation sequencing facilitates quantitative analysis of control and TKO liver transcriptomes
SRA SRX218465
BioSample SAMN01889585

Supplementary file Size Download File type/resource
GSM1067319_5_327_genes.fpkm_tracking.gz 3.8 Mb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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