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| Status |
Public on Mar 09, 2022 |
| Title |
ID109 |
| Sample type |
SRA |
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| Source name |
Roundup_liver
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| Organism |
Rattus norvegicus |
| Characteristics |
group: R50
strain: Sprague-Dawley
tissue: Liver
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| Treatment protocol |
In brief, groups of 12 female Sprague-Dawley rats of 8 weeks of age were treated for 90 days with a mixture of glyphosate (0.5 mg/kg bw/day), azoxystrobin (0.2 mg/kg bw/day), boscalid (0.04 mg/kg bw/day), chlorpyrifos (0.001 mg/kg bw/day), imidacloprid (0.06 mg/kg bw/day), and thiabenzadole (0.1 mg/kg bw/day) via drinking water, and glyphosate (G50) (50 mg/kg bw/day), or its representative EU commercial herbicide formulation Roundup MON 52276 (R50) at the same glyphosate equivalent doses in comparison to a control group (CON).
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| Growth protocol |
The animal study was performed on young adult female Sprague-Dawley rats at the Cesare Maltoni Cancer Research Center, Ramazzini Institute (Bentivoglio, Italy), in accordance with Italian law regulating the use and humane treatment of animals for scientific purposes (Decreto legislativo N. 26, 2014. Attuazione della direttiva n. 2010/63/UE in materia di protezione degli animali utilizzati a fini scientifici. - G.U. Serie Generale, n. 61 del 14 Marzo 2014). The experiment was authorised by the ad hoc commission of the Italian Ministry of Health (authorization N. 447/2018-PR)
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from rat liver tissue excised at the time of sacrifice and which had been stored at -70°C, using the All Prep DNA/RNA/miRNA Universal Kit (Qiagen, Hilden, Germany) using the manufacturer’s instructions. Tissue weight used was ≤ 30 mg, and samples were eluted in 30µl RNase-Free Water. RNA samples were quantified with the Nanodrop 8000 spectrophotometer V2.0 (ThermoScientific, USA) and integrity were checked using the Agilent 2100 Bioanalyser (Agilent Technologies, Waldbronn, Germany). All samples had RNA integrity numbers (RIN) ≥ 7.
We created miRNA libraries from 100 ng total RNA using the QIAseq miRNA library kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. This kit was chosen to incorporate unique molecular indices (UMIs) into each cDNA to enable correction for PCR bias. Library concentrations were measured using Qubit™ dsDNA HS Assay Kit (Thermo Fisher, USA). Size of the libraries and calculation of the final molarity for pooling the libraries for sequencing was performed with the High Sensitivity D1000 ScreenTape Assay on a Agilent 2200 TapeStation System (Agilent Technologies, Waldbronn, Germany). Average sizes of the fragments were 181 ± 22 bp, with TapeStation molarity of of 31.8 ± 12.9 nM.
Libraries were normalised to 3nM before pooling for sequencing. All samples and all libraries were of good quality and 75 bp single reads were generated for each library using the Illumina NextSeq®500 v2.5 High-output 150 cycle kit (Illumina Inc., Cambridge, UK). A total of 111,746,220 reads were generated for these 24 samples (4,656,093 ± 2,282,243 reads per sample).
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
GC.RM.9222.BT5011.109.F.215431_S33_L001_R1_001
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| Data processing |
Analysis of small RNA sequencing data was performed with miRge3.0. This was done in a Conda environment on a Linux machine using the command line version of miRge3.0. We took into account UMIs in order to remove PCR duplicates and used standard small RNA libraries as a reference. The output of miRge3.0 was then imported in R (v4.0.0) for statistical analysis.
Genome_build: MiRge3.0 catalogue
Supplementary_files_format_and_content: umi count data
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| Submission date |
Aug 23, 2021 |
| Last update date |
Mar 09, 2022 |
| Contact name |
Robin Mesnage |
| E-mail(s) |
[email protected]
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| Phone |
+447482206767
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| Organization name |
Kings College London
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| Street address |
Guy's Hospital, 8th Floor, Tower Wing
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| City |
London |
| ZIP/Postal code |
SE1 9RT |
| Country |
United Kingdom |
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| Platform ID |
GPL20084 |
| Series (1) |
| GSE182559 |
miRNA sequencing in liver of rats exposed to glyphosate, MON 52276, and a mixture of pesticides |
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| Relations |
| BioSample |
SAMN20929065 |
| SRA |
SRX11862695 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5531370_GC-RM-9222-BT5011-109-F-215431_S33_L001_R1_001_umiCounts.csv.gz |
36.0 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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