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| Status |
Public on Aug 24, 2018 |
| Title |
Vehicle_3d_NN_IP_Rep5 |
| Sample type |
SRA |
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| Source name |
Vehicle_3d
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
animal id: S011127-214
Sex: Male
age: 6-8 weeks
tissue: Liver
compound: VEHICLE CONTROL
compound abbreviation: CTL_NN
moa: Control
exposure: Control
dose (mg/kg): 0
duration (days): 3
vehicle: SALINE %
nutritive status: Non nutritive
route: ORAL GAVAGE
sample id: 98893
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| Treatment protocol |
Male Sprague-Dawley rats (aged 6–8 weeks and weighing 200–260 g) were dosed once daily in triplicate for 3, 5, or 7 days, depending on the test chemical.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were harvested 24 hours after the last dose 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. Automated RNA isolation was performed according to the manufacture’s protocol using the RNeasy Kit from Qiagen (Germantown, MD).
The sequencing library for the rat liver RNA samples was prepared by BioSpyder (BioSpyder Technologies, Inc., Carlsbad, CA, United States) according to their protocol guidelines. One μl of each RNA sample (500-660 ng/uL) was hybridized with the S1500+ beta detector oligo pool mix (2 μl per sample) using the following thermocycler settings: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, and ending with 45°C for 1 min. Hybridization was followed by nuclease digestion (24 μl nuclease mix addition followed by 90 min at 37°C), ligation (24 μl ligation mix addition followed by 60 min at 37°C, then heat denaturation at 80°C for 30 min).. Ten microliters of each ligation product were then transferred to a 96-well PCR amplification microplate that also contained 10 μl of PCR mix per well. Through amplification well-specific, “barcoded” primer pairs were introduced to templates. Five microliters of the PCR amplification products from each well were then pooled into a single sequencing library. The TempO-Seq library was then processed with a PCR clean-up kit (Machery-Nagel, Mountain View, CA, United States) prior to sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Description |
98893_S78
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| Data processing |
library strategy: TempO-Seq (Templated Oligo assay with Sequencing readout)
Sequencing was performed using a 50 cycle single-end read flow cell on a NextSeq 550 Sequencing System (Illumina, San Diego, CA, united States). Processing of sequencing data was conducted using Illumina’s BCL2FASTQ software employing default parameter settings. Sequencing data were demultiplexed to generate fastq files.
We require that >=75% of the reads have an average quality score >=QC30. The sequences were then filtered for Illumina p5 and p7 adaptors.
Bowtie2-2.1.0
Aligned to a pseudogenome (indexed probe fasta file reflecting the 50 nt sequences targeted by the detector oligos). Indels not allowed. Up to 2 base pair mismatches allowed. Multimapping sequences not allowed.
The counts were summarized using QuasR version 1.8.4.
Genome_build: pseudogenome (indexed probe fasta file reflecting the 50 nt sequences targeted by the detector oligos)
Supplementary_files_format_and_content: tab-delimited text file with read count per gene
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| Submission date |
Aug 23, 2018 |
| Last update date |
May 08, 2019 |
| Contact name |
Pierre Robert Bushel |
| E-mail(s) |
[email protected]
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| Phone |
919-316-4564
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| Organization name |
NIEHS
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| Department |
Biostatistics and Computational Biology Branch
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| Lab |
Bioinformatics
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| Street address |
P.O. Box 12233
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| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platform ID |
GPL25029 |
| Series (1) |
| GSE118956 |
TempO-Seq S1500+ Platform Gene Expression of Rat Liver Mode of Action Samples |
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| Relations |
| BioSample |
SAMN09903522 |
| SRA |
SRX4602851 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3354693_98893_readcounts.txt.gz |
10.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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