|
| Status |
Public on Oct 14, 2015 |
| Title |
Liver_Control_FFPE18h_04_polyA-RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6C3F1
gender: female
age: 5-6 weeks
tissue: liver
|
| Treatment protocol |
Mice were dosed via oral gavage for 21 days. Treated animals were exposed to 8 mg/kg bw/day furan in corn oil. Control animals were gavaged with cornoil oil only. Tissues were collected 4 hours following the final dose.
|
| Growth protocol |
5-6 week old female specific pathogen free B6C3F1 mice were purchased from Charles River Breeding Laboratories (Portage, ME) and were allowed to acclimatize for at least 7 days prior to the start of the study. Feed (NIH-07; Zeigler Brothers, Inc., Gardners, PA) and tap water were available ad libitum. Mice were housed five per cage in polycarbonate cages in a specific pathogen free (SPF) and Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) accredited facility. All procedures were conducted in compliance with the Animal Welfare Act Regulations (9CFR1–4). Mice were handled and treated according to the guidelines provided in the National Institute of Health (NIH) Guide for the Care and Use of Laboratory Animals (ILAR, 1996; http://dels.nas.edu/ilar/).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were anaesthetized under carbon dioxide inhalation followed by exsanguination. Livers were removed and divided into three: One piece was frozen, one piece was preserved in formalin for 18 hours, one piece was preserved in formalin for 3 weeks. FROZEN: samples were placed in cryovials and immediately snap frozen in liquid nitrogen, these tissues were stored at -80oC until RNA extraction was performed. Total RNA was extracted from ~100mg frozen tissue using the RNeasy Midi Kit (Qiagen) according to the manufacturer's instructions. Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively. Fresh-frozen RNA samples had A260/280 ratios > 1.83 and RINs > 8.9. FFPE: samples were preserved in formalin for 18 hours or 3 weeks and then stored in paraffin blocks at room temperature. RNA was extracted from 1x10uM section (18 hours samples) and 2x10uM sections (3 weeks samples) using the RNeasy FFPE RNA extraction kit (Qiagen). Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively. FFPE RNA samples had A260/280 ratios > 1.74 and RINs 1.3-2.4.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Kit v2 (Part# RS-122-2001). Briefly, poly(A)+ mRNA was selected via oligo(dT) beads, fragmented, and converted into ds-cDNA. The resultant cDNAs were barcoded and ligated to Illumina adapters. After adapter ligation, the cDNA was PCR amplified. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA from FFPE livers
polyA RNA enrichment
|
| Data processing |
Basecalls performed using RTA version 1.9
Reads were demultiplexed and converted into fastq files using CASAVA version 1.8.2
RNA-seq reads were aligned to the mm9 genome assembly using STAR version 2.3.0 with default parameters
Counts per gene were calculated using a featureCounts version 1.4.4. 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 for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited matrix which includes counts per gene for each Sample
|
| |
|
| Submission date |
Dec 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Anna Francina Jackson |
| E-mail(s) |
francina.jackson@hc-sc.gc.ca
|
| Organization name |
Health Canada
|
| Department |
Environmental Health Center
|
| Lab |
Dr. Carole Yauk
|
| Street address |
50 Colombine Drive, Tunney's Pasture
|
| City |
Ottawa |
| State/province |
Ontario |
| ZIP/Postal code |
K1A 0K9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE62843 |
Global gene expression analysis in paired fresh-frozen and FFPE furan-exposed mouse liver samples |
| GSE64371 |
Global gene expression analysis of fresh-frozen, furan-exposed mouse liver using RNA-seq [polyA enrichment] |
|
| Relations |
| BioSample |
SAMN03269257 |
| SRA |
SRX818610 |
