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| Status |
Public on Nov 06, 2021 |
| Title |
488 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
Sex: Male
diet: HFHC diet [Rodent diet with 60 kcal% Fat, 10 g Cholesterol and 4g NaCholate; Catalog #D06061401; Research Diets]
treatment: Microcystin-LR (MCLR) [30 µg/kg; Catalog #10007188; Cayman Chemicals]
dose volume: 5 mL/kg
time: 4 week recovery after MCLR
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| Treatment protocol |
Animals were divided into two groups (n=36 per diet group) and fed (ad-libitum) either a control diet or HFHC diet for 8 weeks. Following 8 week diet period, animals were administered vehicle or MCLR via intraperitoneal injections every 48 hours for 2 weeks. Animals were euthanized at three recovery time points: 24 hours (0 week recovery), 2 weeks (2 week recovery) and 4 weeks (4 week recovery) (n=6 per diet and treatment group) after the last MCLR administration.
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| Growth protocol |
Eight-week old male Sprague Dawley rats (n=72) were purchased from Envigo and were maintained in 12 hour light and dark cycles. Handling, care, and maintenance of the animals was done in the Association for the Assessment of Laboratory Animal Care International accredited program of the Laboratory Animal Resources facility of Washington State University (WSU), Spokane. All aspects of the animal research were approved by the Institutional Animal Care and Use Committee at Washington State University (approval code 04937).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were removed and flash frozen. RNA was extracted with TRIzol reagent from frozen liver tissue according to the manufacturers instructions
mRNA libraries were generated from 1.5 µg using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following standard procedures.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Initial adapter trimming and fastq formatting was completed with bcl2fastq (v2.17.1.14)
Further adapter trimming and removal of invariant 100th base position of sequencing reads was completed with Trimmomatic (v.0.38) in single-end mode with parameters -phred33 ILLUMINACLIP:TruSeq_i7adapt_SE-MCLR.fa:2:30:10 CROP:99 and a custom adapter file with longer matches to the Illumina adapter sequences used, after which files were concatenated together by sample.
Sequencing reads were aligned to the rat genome (Rnor6.0; Ensembl release 98) using STAR (v. 2.7.3a) with parameters --outMultimapperOrder Random --outSAMtype BAM
Read counts were obtained with featureCounts (Subread 2.0.0) with parameters -s 2 -t exon -g gene_id
Differential gene expression was calculated with DESeq2 (Bioconductor v. 3.10) with "treatment" as a variable (combined dose, diet, post-exposure recovery time) using the Wald test, normal log fold-change (LFC) shrinkage, an LFC threshold of 0.585 (1.5-fold change), and the Benjamini-Hochberg multiple test correction.
Genome_build: Rnor 6.0; Ensembl release 98
Supplementary_files_format_and_content: trim99_recovery.fCounts is a csv file with 1 row per gene of the Ensembl rat build and columns describing:
Supplementary_files_format_and_content: 1) the genes, including the Ensembl Gene Identifier (Geneid), chromosome (Chr), start base position(Start), end base position (End), Strand, and gene length (Length), and
Supplementary_files_format_and_content: 2) 1 column per sample in the study where cell values correspond to the raw counts calculated by featureCounts for each gene for that sample.
Supplementary_files_format_and_content: DGE_tWsN_results is a csv file with 1 row per gene of the Ensembl rat build and column describing:
Supplementary_files_format_and_content: 1) the genes, including the Ensembl Gene Identifier (Geneid), entrezgene identifier (entrezgene_id), accession names (entrezgene_accession), description of the genes,
Supplementary_files_format_and_content: 2) log fold change (LFC) of gene expression comparing HFHC vehicle group versus Control vehicle group after 0 weeks (Column E), 2 weeks (Column M) and 4 weeks (Column U) of recovery and their associated p-adjusted values (Columns F, N and V respectively),
Supplementary_files_format_and_content: 3) log fold change (LFC) of gene expression comparing Control MCLR group versus Control vehicle group after 0 weeks (Column G), 2 weeks (Column O) and 4 weeks (Column W) of recovery and their associated p-adjusted values (Columns H,P and X respectively),
Supplementary_files_format_and_content: 4) log fold change (LFC) of gene expression comparing HFHC MCLR group versus HFHC vehicle group after 0 weeks (Column I), 2 weeks (Column Q) and 4 weeks (Column Y) of recovery and their associated p-adjusted values (Columns J, R and Z respectively),
Supplementary_files_format_and_content: 5) log fold change (LFC) of gene expression comparing HFHC MCLR group versus Control MCLR group after 0 weeks (Column K), 2 weeks (Column S) and 4 weeks (Column AA) of recovery and their associated p-adjusted values (Columns L, T and AB respectively).
Supplementary_files_format_and_content: DGE_tWsN-VST-ctrl_veh_median_normalized is a csv file describing:
Supplementary_files_format_and_content: Row 1(wks_recovery): Number of weeks after recovery from MCLR exposure (0, 2 or 4)
Supplementary_files_format_and_content: Row 2(diet): The diet each animal received, Control (ctrl) or High fat high cholesterol (HFHC)
Supplementary_files_format_and_content: Row 3(dose): The type of dose treatment received by each animal, Vehicle (veh) or MCLR
Supplementary_files_format_and_content: Row 4 (animal): The number designated to each rat in the study
Supplementary_files_format_and_content: Row 5 and below The Ensembl Gene Identifier of each genes (Column A), followed by the normalized median reads of the gene expression.
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| Submission date |
Nov 04, 2021 |
| Last update date |
Nov 06, 2021 |
| Contact name |
John D. Clarke |
| E-mail(s) |
j.clarke@wsu.edu
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| Organization name |
Washington State University
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| Department |
Pharmaceutical Sciences
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| Lab |
Clarke Lab
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| Street address |
412 E. Spokane Falls Blvd., 412 E. Spokane Fall BLVD
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| City |
Spokane |
| State/province |
Washington |
| ZIP/Postal code |
99202 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE188231 |
MCLR-elicited hepatic fibrosis and carcinogenic gene expression changes persist in rats with diet-induced nonalcoholic steatohepatitis through a 4-week recovery period |
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| Relations |
| BioSample |
SAMN22895890 |
| SRA |
SRX12975675 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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