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Status |
Public on Jul 12, 2014 |
Title |
control cycling 1 |
Sample type |
SRA |
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Source name |
liver
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Organism |
Mus musculus |
Characteristics |
tissue: liver genotype: cTKO cell cycle state: cycling treatment: 48 hrs after CCl4
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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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
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Submission date |
Jan 18, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Julien Sage |
E-mail(s) |
julsage@stanford.edu
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Phone |
(650) 723-5113
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Organization name |
Stanford University
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Department |
Pediatrics
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Lab |
Sage
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Street address |
265 Campus Drive, SIM1 G2078
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City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305-5457 |
Country |
USA |
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Platform ID |
GPL13112 |
Series (1) |
GSE43631 |
next generation sequencing facilitates quantitative analysis of control and TKO liver transcriptomes |
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Relations |
SRA |
SRX218464 |
BioSample |
SAMN01889584 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1067318_6_2835_genes.fpkm_tracking.gz |
2.2 Mb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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