NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1336299 Query DataSets for GSM1336299
Status Public on Aug 08, 2014
Title In Vivo Rat Liver Carcinogen (COH_WANG_BC064YACXX_99810_L_CTL_NU_OG_ACAGTG_s_3)
Sample type SRA
 
Source name Liver
Organism Rattus norvegicus
Characteristics tissue: liver
strain: Sprague-Dawley
mode_of_action: Control
chemical: Vehicle
dose: .
vehicle: CORN OIL 100 %
route: ORAL GAVAGE
duration: 3 d
organ_or_cell_type: LIVER
animal_id: XXV040217-005
Sex: M
vehicle_route_designation: NU_OG
rna_id: 99810
rna_quality_rin: 9.5
sequencing_platform: HiSeq 2000
sequencing_date: 12/16/2011
read_depth: 42,018,904
read_length: 2x101 nt
average_insert_length: 171
ercc_spike_in: Mix1
ercc_mapping_ratio: 0.7
Treatment protocol Animals were acclimated for one week to the testing laboratory prior to dosing. After dosing, all liver samples were harvested as 100 mg punches using six millimeter disposable biopsy punches. An appropriately staggered schedule was employed so that the harvest times were accurate to ±30 min of the designed dose-to-harvest interval.
Growth protocol Upon delivery to testing laboratory male B12 (Crl:CD® (SD)|GS BR) were housed individually in hanging, stainless steel, wire-bottom cages in a ventilated room (temperature, 22±3 ◦C; humidity, 30–70%; 12-h light:12-h dark cycle per day, 6:00 a.m.–6:00 p.m.) and received Certified Rodent Diet #5002 (PMI Feeds Inc.. Richmond, IN); chlorinated tap water was available ad libidum.
Extracted molecule total RNA
Extraction protocol Automated RNA isolation was performed according to the manufacture’s protocol using the RNeasy Kit from Qiagen (Germantown, MD).
Library preparation including the mRNA enrichment step was performed according to the manufacture’s protocol using the Illumina TruSeq RNA Sample Preparation Kit and SBS Kit v3 (San Diego, CA). Samples were blinded during the library preparation. Depths of ~23 – 25 million paired-end 100 bp reads were generated for each sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Training Set
Data processing Illumina Casava1.7 software used for basecalling and barcode demulplexing.
Magic pipeline, please see the attached supplementary file for details and source code download link
Aceview 2008 gene models for rat
One sample from the training set for agent "CARBON TETRACHLORIDE" was excluded from analysis and data deposition due to sample mislabeling.
Genome_build: RGSC v3.4, identical to Rn4 for the main chromosomes
Supplementary_files_format_and_content: tab-delimited text files include Magic expression indices for each Sample ...
 
Submission date Feb 27, 2014
Last update date May 15, 2019
Contact name Leming Shi
E-mail(s) lemingshi@fudan.edu.cn
Phone +86-18616827008
Organization name Fudan University
Department School of Life Sciences
Lab Center for Pharmacogenomics
Street address 2005 Songhu Road
City Shanghai
ZIP/Postal code 200438
Country China
 
Platform ID GPL14844
Series (2)
GSE47792 SEQC Project
GSE55347 SEQC Toxicogenomics Study: RNA-Seq data set
Relations
BioSample SAMN02666154
SRA SRX477306

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap