|
| Status |
Public on Aug 08, 2014 |
| Title |
In Vivo Rat Liver Carcinogen (COH_WANG_BC064YACXX_97426_L_CTL_NU_OG_GCCAAT_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: S011211-018
Sex: M
vehicle_route_designation: NU_OG
rna_id: 97426
rna_quality_rin: 9.5
sequencing_platform: HiSeq 2000
sequencing_date: 12/16/2011
read_depth: 63,267,300
read_length: 2x101 nt
average_insert_length: 172
ercc_spike_in: Mix2
ercc_mapping_ratio: 0.91
|
| 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) |
|
| Relations |
| BioSample |
SAMN02666147 |
| SRA |
SRX477292 |
